def index_gvcf(b: hb.batch.Batch,
input_vcf: hb.resource.ResourceFile,
output_vcf_ind_name: str = None,
memory: int = 3,
storage: int = 5,
docker_img: str = None,
out_dir: str = None):
"""
Index a GVCF file
:param b: batch
:param input_vcf: GVCF file to index
:param output_vcf_ind_name: output GVCF index name
:param memory: job memory
:param storage: storage to use fo the job
:param docker_img: image to use for the job
:param out_dir: output directory
:return:
"""
docker_image = docker_img if docker_img else 'us.gcr.io/broad-gatk/gatk:4.2.0.0'
outname = output_vcf_ind_name + '.g.vcf.gz.tbi'
index_gvcf_file = b.new_job(name=f'index-{output_vcf_ind_name}')
index_gvcf_file.image(docker_image)
index_gvcf_file.memory(f'{memory}Gi')
index_gvcf_file.storage(f'{storage}Gi')
index_gvcf_file.command(f'gatk IndexFeatureFile \
-I {input_vcf} \
-O {outname}')
index_gvcf_file.command(f'mv {outname} {index_gvcf_file.ofile}')
b.write_output(index_gvcf_file.ofile,
f'{out_dir}/merged-gvcf/{output_vcf_ind_name}/{outname}')
return index_gvcf_file
def merge_vcf(b: hb.batch.Batch,
gvcf_list: List = None,
output_vcf_name: str = None,
merge_vcfs_img: str = None,
memory: int = 3,
out_dir: str = None,
storage: int = None):
# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
docker_image = merge_vcfs_img if merge_vcfs_img else 'us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.3-1564508330'
outname = output_vcf_name + '.g.vcf.gz'
# disk_size = bytes_to_gb((inputs_vcfs_list * 2.5)) + 10
merge_vcf_i = ''
for line in gvcf_list:
input_gvcf = b.read_input(line)
merge_vcf_i += f'I={input_gvcf} \t'
merge_vcfs = b.new_job(name=output_vcf_name)
merge_vcfs.image(docker_image)
merge_vcfs.memory(f'{memory}Gi')
merge_vcfs.storage(f'{storage}Gi')
merge_vcfs.command(f'java -Xms2000m -jar /usr/gitc/picard.jar \
MergeVcfs \
{merge_vcf_i} \
O={outname}')
merge_vcfs.command(f'mv {outname} {merge_vcfs.ofile}')
b.write_output(merge_vcfs.ofile,
f'{out_dir}/merged-gvcf/{output_vcf_name}/{outname}')
return merge_vcfs
def validate_vcf(b: hb.batch.Batch,
input_vcf: hb.resource.ResourceFile,
ref_fasta: hb.resource.ResourceGroup,
dbsnp_vcf_file: hb.resource.ResourceGroup,
calling_int_file: hb.resource.ResourceFile,
validate_vcf_img: str = None,
memory: int = 7,
storage: int = None,
output_vcf_ind_name: str = None):
# Validate the (g)VCF output of HaplotypeCaller
docker_image = validate_vcf_img if validate_vcf_img else 'us.gcr.io/broad-gatk/gatk:4.2.0.0'
# ref_size = bytes_to_gb(ref_fasta) + bytes_to_gb(ref_fasta_index) + bytes_to_gb(ref_dict)
# disk_size = bytes_to_gb(input_vcf) + bytes_to_gb(dbsnp_vcf) + ref_size + 20
validate_gvcf = b.new_job(name=output_vcf_ind_name)
validate_gvcf.image(docker_image)
validate_gvcf.memory(f'{memory}Gi')
validate_gvcf.storage(f'{storage}Gi')
validate_gvcf.command(f'gatk IndexFeatureFile \
-I {input_vcf}')
validate_gvcf.command(f'gatk --java-options -Xms6000m \
ValidateVariants \
-V {input_vcf} \
-R {ref_fasta.fasta} \
-L {calling_int_file} \
-gvcf \
--validation-type-to-exclude ALLELES \
--dbsnp {dbsnp_vcf_file.vcf}')
return validate_gvcf
def scatter_interval_list(b: hb.batch.Batch,
interval_list_file: hb.resource.ResourceFile,
scatter_count: int = 50,
break_bands_at_multiples_of: int = 1000000,
scatter_img: str = None,
memory: int = 2,
out_dir: str = None):
"""
break the calling interval list into sub-intervals
:param b: batch
:param interval_list_file: one or more interval lists
:param scatter_count: the number of files into which to scatter the resulting list by locus
:param break_bands_at_multiples_of: if set to a positive value will create a new interval list with the original
intervals broken up at integer multiples of this value. Set to 0 to NOT break up intervals
:param scatter_img: image to use for the job
:param memory: job memory
:param out_dir: output directory
:return:
"""
# break the calling interval list into sub-intervals
docker_image = scatter_img if scatter_img else 'us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.3-1564508330'
scatter_list = b.new_job(name='scatter-interval-list')
scatter_list.image(docker_image)
scatter_list.cpu(1)
scatter_list.memory(f'{memory}Gi')
scatter_list.command('mkdir /scatter_intervals')
scatter_list.command(f'java -Xms1g -jar /usr/gitc/picard.jar \
IntervalListTools \
SCATTER_COUNT={scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
UNIQUE=true \
SORT=true \
BREAK_BANDS_AT_MULTIPLES_OF={break_bands_at_multiples_of} \
INPUT={interval_list_file} \
OUTPUT=/scatter_intervals')
scatter_list.command('''
cat > my_script.py <<EOF
import sys
import os
import glob
intervals = sorted(glob.glob('/scatter_intervals/*/*.interval_list'))
for i, interval in enumerate(intervals):
(directory, filename) = os.path.split(interval)
newName = os.path.join(directory, str(i + 1) + filename)
os.rename(interval, newName)
EOF
python3 my_script.py
''')
scatter_list.command(f'mv /scatter_intervals {scatter_list.outfiles}')
b.write_output(scatter_list.outfiles, f'{out_dir}/scatter-intervals')
# We return the `scatter_list` Job object that can be used in downstream jobs.
return scatter_list
def collect_variant_calling_metrics(
b: hb.batch.Batch,
input_vcf: hb.resource.ResourceGroup,
dbsnp_vcf_file: hb.resource.ResourceGroup,
ref_dict: hb.resource.ResourceGroup,
evaluation_int_list: hb.resource.ResourceFile,
metrics_basename: str = None,
memory: int = 6,
docker_img: str = None,
storage: int = None,
out_dir: str = None):
"""
Call germline SNPs and indels
:param b: batch
:param input_vcf: GVCF file to collect variant calling metrics for
:param dbsnp_vcf_file: DBSNP VCF and its index to use in collecting metrics
:param ref_dict: reference dictionary file from a reference Group (fasta, index, and dict) Resource
:param evaluation_int_list: evaluation list file
:param metrics_basename: name to be used for output
:param memory: job memory
:param docker_img: image to use for the job
:param storage: storage to use fo the job
:param out_dir: output directory
:return:
"""
docker_image = docker_img if docker_img else 'us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.3-1564508330'
collect_vc_metrics = b.new_job(name=metrics_basename)
collect_vc_metrics.image(docker_image)
collect_vc_metrics.memory(f'{memory}Gi')
collect_vc_metrics.storage(f'{storage}Gi')
collect_vc_metrics.command(f'java -Xms2000m -jar /usr/gitc/picard.jar \
CollectVariantCallingMetrics \
INPUT={input_vcf.vcf} \
OUTPUT={metrics_basename} \
DBSNP={dbsnp_vcf_file.vcf} \
SEQUENCE_DICTIONARY={ref_dict.dict} \
TARGET_INTERVALS={evaluation_int_list} \
GVCF_INPUT=true')
collect_vc_metrics.command(
f'mv {metrics_basename}.variant_calling_detail_metrics {collect_vc_metrics.detail}'
)
collect_vc_metrics.command(
f'mv {metrics_basename}.variant_calling_summary_metrics {collect_vc_metrics.summary}'
)
b.write_output(
collect_vc_metrics.detail,
f'{out_dir}/variant-calling-metrics/{metrics_basename}/{metrics_basename}.variant_calling_detail_metrics'
)
b.write_output(
collect_vc_metrics.summary,
f'{out_dir}/variant-calling-metrics/{metrics_basename}/{metrics_basename}.variant_calling_summary_metrics'
)
return collect_vc_metrics
def haplotype_caller_gatk(b: hb.batch.Batch,
input_bam: hb.resource.ResourceGroup,
ref_fasta: hb.resource.ResourceGroup,
interval_list_file: hb.resource.ResourceFile,
bam_filename_no_ext: str = None,
out_dir: str = None,
interval_list_name: str = None,
storage: int = None,
contamination: float = None,
gatk_img: str = None,
memory: float = 6.5,
ncpu: int = 2):
"""
Call germline SNPs and indels
:param b: batch
:param input_bam: BAM file
:param ref_fasta: reference files, including fasta and index
:param interval_list_file: interval list file with intervals to run variant calling on
:param bam_filename_no_ext: BAM filename without extension
:param interval_list_name: interval list name, used to name output GVCF
:param storage: storage to use fo the job
:param contamination: fraction of contamination in sequencing data to aggressively remove
:param gatk_img: image to use for the job
:param out_dir: output directory
:param memory: job memory
:param ncpu: number of CPUs
:return:
"""
docker_image = gatk_img if gatk_img else 'us.gcr.io/broad-gatk/gatk:4.2.0.0'
output_file_name = bam_filename_no_ext + '_' + interval_list_name + '.g.vcf.gz'
variant_calling = b.new_job(name=bam_filename_no_ext)
variant_calling.image(docker_image)
variant_calling.cpu(ncpu)
variant_calling.memory(f'{memory}Gi')
variant_calling.storage(f'{storage}Gi')
variant_calling.command(
f'gatk --java-options "-Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
HaplotypeCaller \
-R {ref_fasta.fasta} \
-I {input_bam.bam} \
-L {interval_list_file} \
-O {variant_calling.ofile}\
-contamination {contamination} \
-G StandardAnnotation -G StandardHCAnnotation -G AS_StandardAnnotation \
-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90 \
-ERC GVCF')
# variant_calling.command(f'mv {output_file_name} {variant_calling.ofile}')
b.write_output(
variant_calling.ofile,
f'{out_dir}/variant-calling/{bam_filename_no_ext}/{output_file_name}')
return variant_calling
def imputation(b: hb.batch.Batch,
vcf: str = None,
vcf_filename_no_ext: str = None,
ref: hb.ResourceGroup = None,
ref_size: Union[int, float] = None,
region: str = None,
chromosome: str = None,
cpu: int = 8,
memory: str = 'highmem',
img: str = 'docker.io/lindonkambule/gwaspy:v1',
threads: int = 7,
out_dir: str = None):
# in_vcf = b.read_input(vcf)
in_vcf = b.read_input_group(**{'bcf': vcf, 'bcf.csi': f'{vcf}.csi'})
vcf_size = bytes_to_gb(vcf)
output_file_name = vcf_filename_no_ext + '.imputed.bcf'
file_dir = vcf_filename_no_ext.split('.')[0]
disk_size = ref_size + (vcf_size * 4)
map_file = f'/shapeit4/maps/b38/{chromosome}.b38.gmap.gz'
impute = b.new_job(name=output_file_name)
impute.cpu(cpu)
impute.memory(memory)
impute.storage(f'{disk_size}Gi')
impute.image(img)
cmd = f'''
impute5_1.1.5_static \
--h {ref.bcf} \
--m {map_file} \
--g {in_vcf.bcf} \
--r {region} \
--out-gp-field \
--o {output_file_name} \
--threads {threads}
'''
impute.command(cmd)
# index file to use when merging
impute.command(f'bcftools index {output_file_name}')
impute.command(f'mv {output_file_name} {impute.ofile}')
impute.command(f'mv {output_file_name}.csi {impute.ind}')
b.write_output(
impute.ofile,
f'{out_dir}/GWASpy/Imputation/{file_dir}/imputed_chunks/{output_file_name}'
)
b.write_output(
impute.ind,
f'{out_dir}/GWASpy/Imputation/{file_dir}/imputed_chunks/{output_file_name}.csi'
)
def concat_vcfs(b: hb.batch.Batch,
vcf_basename: str = None,
vcfs_to_merge: List = None,
output_type: str = 'vcf',
chrom: str = None,
cpu: int = 16,
memory: str = 'standard',
docker_img: str = 'docker.io/lindonkambule/gwaspy:v1',
out_dir: str = None):
global index_cmd
out_type = 'b' if output_type == 'bcf' else 'z'
vcfs_sizes_sum = 0
merge_vcf_i = ''
out_filename = f'{vcf_basename}.{chrom}.merged.bcf' if output_type == 'bcf' else \
f'{vcf_basename}.{chrom}.merged.vcf.gz'
out_index_name = f'{vcf_basename}.{chrom}.merged.bcf.csi' if output_type == 'bcf' else \
f'{vcf_basename}.{chrom}.merged.vcf.gz.csi'
for line in vcfs_to_merge:
vcfs_sizes_sum += 2 + bytes_to_gb(line)
disk_size = int(round(10 + (2 * vcfs_sizes_sum)))
threads = cpu - 1
concat = b.new_job(name=f'concat-{vcf_basename}')
concat.memory(memory)
concat.storage(f'{disk_size}Gi')
concat.image(docker_img)
concat.cpu(cpu)
for line in vcfs_to_merge:
input_vcf = b.read_input_group(vcf=line,
ind=f'{line}.csi')
merge_vcf_i += f'{input_vcf.vcf} '
cmd = f'''
bcftools concat \
--no-version \
--output-type {out_type} \
--output {out_filename} \
--threads {threads} \
{merge_vcf_i}
'''
concat.command(cmd)
# index the merged output
concat.command(f'bcftools index --force {out_filename}')
concat.command(f'mv {out_filename} {concat.ofile}')
concat.command(f'mv {out_index_name} {concat.idx}')
b.write_output(concat.ofile, f'{out_dir}/GWASpy/{vcf_basename}/Imputation/imputed_merged/{out_filename}')
b.write_output(concat.idx, f'{out_dir}/GWASpy/{vcf_basename}/Imputation/imputed_merged/{out_index_name}')
def aut_impute(b: hb.batch.Batch,
vcf: hb.ResourceGroup = None,
vcf_filename_no_ext: str = None,
ref: hb.ResourceGroup = None,
region: str = None,
chromosome: str = None,
buffer: int = 250,
storage: int = None,
memory: str = None,
cpu: int = None,
img: str = 'docker.io/lindonkambule/gwaspy:v1',
out_dir: str = None):
out_file_name = vcf_filename_no_ext + '.imputed.bcf'
file_dir = vcf_filename_no_ext.split('.')[0]
map_file = f'/shapeit4/maps/b38/{chromosome}.b38.gmap.gz'
threads = cpu - 1
impute = b.new_job(name=out_file_name)
impute.cpu(cpu)
impute.memory(memory)
impute.storage(f'{storage}Gi')
impute.image(img)
cmd = f'''
impute5_1.1.5_static \
--h {ref.bcf} \
--m {map_file} \
--g {vcf.bcf} \
--r {region} \
--out-gp-field \
--o {out_file_name} \
--b {buffer} \
--threads {threads}
'''
impute.command(cmd)
# index file to use when merging
impute.command(f'bcftools index {out_file_name}')
impute.command(f'mv {out_file_name} {impute.ofile}')
impute.command(f'mv {out_file_name}.csi {impute.idx}')
b.write_output(
impute.ofile,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}'
)
b.write_output(
impute.idx,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}.csi'
)
def clump(batch: hb.batch.Batch, image: str, bfile: hb.resource.ResourceGroup, assoc: hb.resource.ResourceFile, chr: int) -> hb.job.Job:
"""
Clump association results with PLINK.
https://zzz.bwh.harvard.edu/plink/clump.shtml
"""
# Define a new job `c` in Batch `batch` with name `clump-CHR`
c = batch.new_job(name=f'clump-{chr}')
# TODO: Tell the new `c` job the location of the image of where you pushed your image in GCR that contains your Hail script
# This image name is defined by the `image` variable as an argument to the function
c.image(image)
# Tell Batch to use 1Gi of memory for this job
c.memory('1Gi')
# Tell Batch to use 1 cpu for this job
c.cpu(1)
# Notice that we can simply call plink2 here because we put it on the PATH in the Dockerfile
# TODO: Fill in the argument <BFILE> which uses the `bfile` argument we passed in to the function above.
# `bfile` is a resource group and is expected to have three files at a common root name: {root}.bed, {root}.bim, {root}.fam
# TODO: Fill in the argument <ASSOC> which uses the `assoc` argument we passed in to the function above. This file has the p-values of the GWAS.
# TODO: Fill in the argument <CHR> which uses the `chr` we passed in to the function above. This will tell PLINK to only compute
# the clumping results for this chromosome. This is how we achieve parallelism by chromosome.
c.command(f'''
plink --bfile {bfile} \
--clump {assoc} \
--chr {chr} \
--clump-p1 0.0001 \
--clump-p2 0.001 \
--clump-r2 0.5 \
--clump-kb 1000 \
--memory 1024 \
--threads 1
mv plink.clumped {c.clumped} || \
echo " CHR F SNP BP P TOTAL NSIG S05 S01 S001 S0001 SP2" > {c.clumped}
''')
# PLINK outputs the results at a hardcoded path. So we'll move it to a path Batch will know to copy.
# PLINK doesn't output a file if there are no results so we'll make one
# We return the `c` Job object that can be used in downstream jobs.
return c
def scatter_interval_list(b: hb.batch.Batch,
interval_list_file: hb.resource.ResourceFile,
scatter_count: int = 50,
break_bands_at_multiples_of: int = 1000000,
scatter_img: str = None,
memory: int = 2,
out_dir: str = None):
# break the calling interval list into sub-intervals
docker_image = scatter_img if scatter_img else 'us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.3-1564508330'
scatter_list = b.new_job(name='scatter-interval-list')
scatter_list.image(docker_image)
scatter_list.cpu(1) # this should be lower, check DSP pipeline
scatter_list.memory(f'{memory}Gi')
scatter_list.command('mkdir /scatter_intervals')
scatter_list.command(f'java -Xms1g -jar /usr/gitc/picard.jar \
IntervalListTools \
SCATTER_COUNT={scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
UNIQUE=true \
SORT=true \
BREAK_BANDS_AT_MULTIPLES_OF={break_bands_at_multiples_of} \
INPUT={interval_list_file} \
OUTPUT=/scatter_intervals')
scatter_list.command('''
cat > my_script.py <<EOF
import sys
import os
import glob
intervals = sorted(glob.glob('/scatter_intervals/*/*.interval_list'))
for i, interval in enumerate(intervals):
(directory, filename) = os.path.split(interval)
newName = os.path.join(directory, str(i + 1) + filename)
os.rename(interval, newName)
EOF
python3 my_script.py
''')
scatter_list.command(f'mv /scatter_intervals {scatter_list.outfiles}')
b.write_output(scatter_list.outfiles, f'{out_dir}/scatter-intervals')
# We return the `scatter_list` Job object that can be used in downstream jobs.
return scatter_list
def run_gwas(batch: hb.batch.Batch, image: str, vcf: hb.resource.ResourceFile, phenotypes: hb.resource.ResourceFile) -> hb.job.Job:
"""
QC data
Get association test statistics
Also, export PLINK file
"""
# TODO: Take the input batch and create a new job object called `gwas`. You can give it the name 'run-gwas'
# which will be useful when looking at the Batch UI to see what job corresponds to your code.
gwas = batch.new_job(name='run-gwas')
# TODO: Tell the new `gwas` job the image name of where you pushed your image in GCR that contains your Hail script
# This image name is defined by the `image` variable as an argument to the function
gwas.image(image)
# This is how we tell Batch that we want this job to have 4 cores. This number must match the argument
# to `gwas_hail.py`, which tells Hail to run in local mode with 4 cores available.
gwas.cpu(4)
# This is how we tell Batch that we're defining a new ResourceGroup that is the output of the `gwas` Job.
# PLINK will output four files here with a common root name. We designate this common file root with `{root}`
# and hard code the extensions pertaining to each file. Now we can reference the common file root as `gwas.ofile`
# To reference the bim file specifically, we can use `gwas.ofile.bim` or `gwas.ofile['bim']`
gwas.declare_resource_group(ofile={
'bed': '{root}.bed',
'bim': '{root}.bim',
'fam': '{root}.fam',
'assoc': '{root}.assoc'
})
# The command definition below uses f-strings. The contents in between curly braces ({, }) are evaluated as Python expressions.
# TODO: Fill in the <PATH> to the Python script `gwas_hail.py` with its location in the Docker image specified above.
# TODO: Fill in the argument <VCF> which represents the VCF file we passed in to the function above.
# TODO: Fill in the argument <OUTPUT_FILE> to the `--output-file` argument below. This should be the file root of the resource group declared above.
gwas.command(f'''
python3 /gwas_hail.py \
--vcf {vcf} \
--phenotypes {phenotypes} \
--output-file {gwas.ofile} \
--cores 4
''')
# We return the `gwas` Job object that can be used in downstream jobs.
return gwas
def merge_vcf(b: hb.batch.Batch,
gvcf_list: List = None,
output_vcf_name: str = None,
merge_vcfs_img: str = None,
memory: int = 3,
out_dir: str = None,
storage: int = None):
"""
Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
:param b: batch
:param gvcf_list: list of GVCF files to merge
:param output_vcf_name: output GVCF name
:param merge_vcfs_img: image to use for the job
:param storage: Storage to use fo the job
:param out_dir: output directory
:param memory: job memory
:return:
"""
docker_image = merge_vcfs_img if merge_vcfs_img else\
'us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.3-1564508330'
outname = output_vcf_name + '.g.vcf.gz'
merge_vcf_i = ''
for line in gvcf_list:
input_gvcf = b.read_input(line)
merge_vcf_i += f'I={input_gvcf} \t'
merge_vcfs = b.new_job(name=output_vcf_name)
merge_vcfs.image(docker_image)
merge_vcfs.memory(f'{memory}Gi')
merge_vcfs.storage(f'{storage}Gi')
merge_vcfs.command(f'java -Xms2000m -jar /usr/gitc/picard.jar \
MergeVcfs \
{merge_vcf_i} \
O={outname}')
merge_vcfs.command(f'mv {outname} {merge_vcfs.ofile}')
b.write_output(merge_vcfs.ofile,
f'{out_dir}/merged-gvcf/{output_vcf_name}/{outname}')
return merge_vcfs
def collect_variant_calling_metrics(
b: hb.batch.Batch,
input_vcf: hb.resource.ResourceGroup,
dbsnp_vcf_file: hb.resource.ResourceGroup,
ref_dict: hb.resource.ResourceGroup,
evaluation_int_list: hb.resource.ResourceFile,
metrics_basename: str = None,
memory: int = 6,
docker_img: str = None,
storage: int = None,
out_dir: str = None):
docker_image = docker_img if docker_img else 'us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.3-1564508330'
collect_vc_metrics = b.new_job(name=metrics_basename)
collect_vc_metrics.image(docker_image)
collect_vc_metrics.memory(f'{memory}Gi')
collect_vc_metrics.storage(f'{storage}Gi')
collect_vc_metrics.command(f'java -Xms2000m -jar /usr/gitc/picard.jar \
CollectVariantCallingMetrics \
INPUT={input_vcf.vcf} \
OUTPUT={metrics_basename} \
DBSNP={dbsnp_vcf_file.vcf} \
SEQUENCE_DICTIONARY={ref_dict.dict} \
TARGET_INTERVALS={evaluation_int_list} \
GVCF_INPUT=true')
# collect_vc_metrics.command(f'ls')
collect_vc_metrics.command(
f'mv {metrics_basename}.variant_calling_detail_metrics {collect_vc_metrics.detail}'
)
collect_vc_metrics.command(
f'mv {metrics_basename}.variant_calling_summary_metrics {collect_vc_metrics.summary}'
)
b.write_output(
collect_vc_metrics.detail,
f'{out_dir}/variant-calling-metrics/{metrics_basename}/{metrics_basename}.variant_calling_detail_metrics'
)
b.write_output(
collect_vc_metrics.summary,
f'{out_dir}/variant-calling-metrics/{metrics_basename}/{metrics_basename}.variant_calling_summary_metrics'
)
return collect_vc_metrics
def cram_to_bam(b: hb.batch.Batch,
input_cram_file: str = None,
ref_fasta: str = None,
ref_dict: str = None,
ref_ind: str = None,
bam_out_name: str = None,
memory: int = 15,
samtools_image: str = None,
out_dir: str = None):
docker_image = samtools_image if samtools_image else 'gcr.io/genomics-tools/samtools'
out_bam_name = bam_out_name + '.bam'
output_bam_size: float = bytes_to_gb(input_cram_file) / 0.40
ref_size: float = bytes_to_gb(ref_fasta) + bytes_to_gb(ref_ind)
disk_size: int = round(
bytes_to_gb(input_cram_file) + output_bam_size + ref_size) + 25
job_memory = str(memory) + 'Gi'
job_storage = str(disk_size) + 'Gi'
crams_to_bams = b.new_job(name=out_bam_name)
in_cram = b.read_input(input_cram_file)
fasta = b.read_input_group(**{
'fasta': ref_fasta,
'fasta.fai': ref_ind,
'dict': ref_dict
})
crams_to_bams.memory(job_memory)
crams_to_bams.image(docker_image)
crams_to_bams.storage(job_storage)
crams_to_bams.command(
f'samtools view -b -T {fasta.fasta} -o {out_bam_name} {in_cram}')
crams_to_bams.command(f'samtools index {out_bam_name}')
crams_to_bams.command(f'mv {out_bam_name} {crams_to_bams.bamout}')
crams_to_bams.command(f'mv {out_bam_name}.bai {crams_to_bams.bamind}')
b.write_output(crams_to_bams.bamout, f'{out_dir}/BAMS/{out_bam_name}')
b.write_output(crams_to_bams.bamind, f'{out_dir}/BAMS/{out_bam_name}.bai')
return crams_to_bams
def haplotype_caller_gatk(b: hb.batch.Batch,
input_bam: hb.resource.ResourceGroup,
ref_fasta: hb.resource.ResourceGroup,
interval_list_file: hb.resource.ResourceFile,
bam_filename_no_ext: str = None,
out_dir: str = None,
interval_list_name: str = None,
storage: int = None,
contamination: float = None,
gatk_img: str = None,
memory: float = 6.5,
ncpu: int = 2):
docker_image = gatk_img if gatk_img else 'us.gcr.io/broad-gatk/gatk:4.2.0.0'
output_file_name = bam_filename_no_ext + '_' + interval_list_name + '.g.vcf.gz'
variant_calling = b.new_job(name=bam_filename_no_ext)
variant_calling.image(docker_image)
variant_calling.cpu(ncpu)
variant_calling.memory(f'{memory}Gi')
variant_calling.storage(f'{storage}Gi')
variant_calling.command(
f'gatk --java-options "-Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
HaplotypeCaller \
-R {ref_fasta.fasta} \
-I {input_bam.bam} \
-L {interval_list_file} \
-O {variant_calling.ofile}\
-contamination {contamination} \
-G StandardAnnotation -G StandardHCAnnotation -G AS_StandardAnnotation \
-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90 \
-ERC GVCF')
# variant_calling.command(f'mv {output_file_name} {variant_calling.ofile}')
b.write_output(
variant_calling.ofile,
f'{out_dir}/variant-calling/{bam_filename_no_ext}/{output_file_name}')
# We return the `variant_calling` Job object that can be used in downstream jobs.
return variant_calling
def index_gvcf(b: hb.batch.Batch,
input_vcf: hb.resource.ResourceFile,
output_vcf_ind_name: str = None,
memory: int = 3,
storage: int = 5,
docker_img: str = None,
out_dir: str = None):
docker_image = docker_img if docker_img else 'us.gcr.io/broad-gatk/gatk:4.2.0.0'
outname = output_vcf_ind_name + '.g.vcf.gz.tbi'
index_gvcf_file = b.new_job(name=f'index-{output_vcf_ind_name}')
index_gvcf_file.image(docker_image)
index_gvcf_file.memory(f'{memory}Gi')
index_gvcf_file.storage(f'{storage}Gi')
index_gvcf_file.command(f'gatk IndexFeatureFile \
-I {input_vcf} \
-O {outname}')
index_gvcf_file.command(f'mv {outname} {index_gvcf_file.ofile}')
b.write_output(index_gvcf_file.ofile,
f'{out_dir}/merged-gvcf/{output_vcf_ind_name}/{outname}')
return index_gvcf_file
def validate_vcf(b: hb.batch.Batch, input_vcf: hb.resource.ResourceFile, ref_fasta: hb.resource.ResourceGroup,
dbsnp_vcf_file: hb.resource.ResourceGroup, calling_int_file: hb.resource.ResourceFile,
validate_vcf_img: str = None, memory: int = 7, storage: int = None,
output_vcf_ind_name: str = None):
"""
Validate the GVCF output of HaplotypeCaller
:param b: batch
:param input_vcf: GVCF file to validate
:param ref_fasta: reference files, including fasta and index
:param dbsnp_vcf_file: DBSNP VCF and its index to use in the validation
:param calling_int_file: calling interval file
:param validate_vcf_img: image to use for the job
:param memory: job memory
:param storage: storage to use fo the job
:param output_vcf_ind_name: name to be used for the job
:return:
"""
docker_image = validate_vcf_img if validate_vcf_img else 'us.gcr.io/broad-gatk/gatk:4.2.0.0'
validate_gvcf = b.new_job(name=output_vcf_ind_name)
validate_gvcf.image(docker_image)
validate_gvcf.memory(f'{memory}Gi')
validate_gvcf.storage(f'{storage}Gi')
validate_gvcf.command(f'gatk IndexFeatureFile \
-I {input_vcf}')
validate_gvcf.command(f'gatk --java-options -Xms6000m \
ValidateVariants \
-V {input_vcf} \
-R {ref_fasta.fasta} \
-L {calling_int_file} \
-gvcf \
--validation-type-to-exclude ALLELES \
--dbsnp {dbsnp_vcf_file.vcf}')
return validate_gvcf
def merge(batch: hb.batch.Batch, results: List[hb.resource.ResourceFile]) -> hb.job.Job:
"""
Merge clumped results files together
"""
# Define a new job `merger` in Batch `batch` with name `merge-results`
merger = batch.new_job(name='merge-results')
# Use the ubuntu:18.04 image which Batch caches
merger.image('ubuntu:18.04')
# Do some file munging to concatenate all of the clumped results together for all chromosomes
if results:
merger.command(f'''
head -n 1 {results[0]} > {merger.ofile}
for result in {" ".join(results)}
do
tail -n +2 "$result" >> {merger.ofile}
done
sed -i '/^$/d' {merger.ofile}
''')
# We return the `merger` Job object that can be used in downstream jobs.
return merger
def sex_impute(b: hb.batch.Batch,
vcf: hb.ResourceGroup = None,
vcf_filename_no_ext: str = None,
females_list: hb.ResourceFile = None,
ref: hb.ResourceGroup = None,
region: str = None,
buffer: int = 250,
storage: int = None,
memory: str = None,
cpu: int = None,
img: str = 'docker.io/lindonkambule/gwaspy:v1',
out_dir: str = None):
global cmd
in_females = females_list
out_file_name = vcf_filename_no_ext + '.imputed.bcf'
file_dir = vcf_filename_no_ext.split('.')[0]
threads = cpu - 1
impute = b.new_job(name=out_file_name)
impute.cpu(cpu)
impute.memory(memory)
impute.storage(f'{storage}Gi')
impute.image(img)
start = int(region.split(':')[1].split('-')[0])
end = int(region.split(':')[1].split('-')[1])
# A. PAR1 REGION ONLY
if end <= 2781479:
# run diploid imputation
impute.command(
'echo THIS CHUNK IS IN PAR1 REGION, SO WE WILL RUN DIPLOID IMPUTATION'
)
map_file = '/shapeit4/maps/b38/chrX_par1.b38.gmap.gz'
if start < 10001:
start_new = 10001
end_new = end
else:
start_new = start
end_new = end
new_imp_region = f'chrX:{start_new}-{end_new}'
cmd = f'''
impute5_1.1.5_static \
--h {ref.bcf} \
--m {map_file} \
--g {vcf.bcf} \
--r {new_imp_region} \
--out-gp-field \
--o {out_file_name} \
--b {buffer} \
--threads {threads}
'''
impute.command(cmd)
# index file to use when merging
impute.command(f'bcftools index {out_file_name}')
impute.command(f'mv {out_file_name} {impute.ofile}')
impute.command(f'mv {out_file_name}.csi {impute.idx}')
b.write_output(
impute.ofile,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}'
)
b.write_output(
impute.idx,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}.csi'
)
# B. PAR2 REGION ONLY
elif start >= 155701383:
# run diploid imputation
impute.command(
'echo THIS CHUNK IS IN PAR2 REGION, SO WE WILL RUN DIPLOID IMPUTATION'
)
map_file = '/shapeit4/maps/b38/chrX_par2.b38.gmap.gz'
if end > 156030895:
end_new = 156030895
start_new = start
else:
start_new = start
end_new = end
new_imp_region = f'chrX:{start_new}-{end_new}'
cmd = f'''
impute5_1.1.5_static \
--h {ref.bcf} \
--m {map_file} \
--g {vcf.bcf} \
--r {new_imp_region} \
--out-gp-field \
--o {out_file_name} \
--b {buffer} \
--threads {threads}
'''
impute.command(cmd)
# index file to use when merging
impute.command(f'bcftools index {out_file_name}')
impute.command(f'mv {out_file_name} {impute.ofile}')
impute.command(f'mv {out_file_name}.csi {impute.idx}')
b.write_output(
impute.ofile,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}'
)
b.write_output(
impute.idx,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}.csi'
)
# C. NON-PAR REGION ONLY
elif (start >= 2781479) & (end <= 155701382):
map_file = '/shapeit4/maps/b38/chrX.b38.gmap.gz'
start_new = start
end_new = end
new_imp_region = f'chrX:{start_new}-{end_new}'
# (1) split by sex NB: THE USER SHOULD SUPPLY A FILE CONTAINING EITHER ONLY FEMALES OR MALE SAMPLE IDS
# WITH ONE SAMPLE ID PER LINE
cmd_split = f'''
echo THIS CHUNK IS ONLY IN THE NON-PAR REGION, SO WE WILL SPLIT IT BY SEX BEFORE RUNNING IMPUTATION
echo GETTING THE ORDER OF SAMPLES
bcftools query -l {vcf.bcf} > samples_order.txt
echo SPLITTING SAMPLES BY SEX
bcftools view -S {in_females} {vcf.bcf} --output-type b --output females.bcf
bcftools view -S ^{in_females} {vcf.bcf} --output-type b --output males.bcf
echo INDEXING THE FILES BEFORE RUNNING IMPUTATION
bcftools index females.bcf
bcftools index males.bcf
'''
impute.command(cmd_split)
# (2) run imputation separately for females and males
cmd_impute = f'''
impute5_1.1.5_static --h {ref.bcf} --m {map_file} --g females.bcf --r {new_imp_region} --out-gp-field \
--o females.imputed.bcf --b {buffer} --threads {threads}
impute5_1.1.5_static --h {ref.bcf} --m {map_file} --g males.bcf --r {new_imp_region} --out-gp-field \
--o males.imputed.bcf --b {buffer} --threads {threads} -- haploid
'''
impute.command(cmd_impute)
# (3) merge the imputed files back together into one chunk
# (3a) index females and males files to be merged and create a file with these for bcftools
cmd_index_chunks = f'''
bcftools index females.imputed.bcf
bcftools index males.imputed.bcf
rm females.bcf* males.bcf*
'''
impute.command(cmd_index_chunks)
# (3b) sometimes there are duplicates (raw and imputed with flipped alleles) and this causes an error when
# merging, so we remove any duplicates
cmd_sort = f'''
echo CHECKING FOR DUPLICATE VARIANTS AND REMOVING THEM
bcftools norm -d any females.imputed.bcf --output-type b --output females.imputed.sorted.bcf
rm females.imputed.bcf*
bcftools norm -d any males.imputed.bcf --output-type b --output males.imputed.sorted.bcf
rm males.imputed.bcf*
bcftools index females.imputed.sorted.bcf
bcftools index males.imputed.sorted.bcf
echo -e "females.imputed.sorted.bcf\nmales.imputed.sorted.bcf" > merge.txt
'''
impute.command(cmd_sort)
# (3c) merge the files into one
cmd_merge = f'''
echo MERGING THE MALES AND FEMALES FILE BACK TOGETHER
bcftools merge --file-list merge.txt --output-type b --output merged.sex.bcf
'''
impute.command(cmd_merge)
# (3d) reorder samples back to how they were initially
# splitting and re-merging samples will result in change in order compared to the initial file
# so we have to use the initial samples order for the concat step by chromosome of imputation
cmd_order = f'''
echo ORDERING SAMPLES TO HOW THEY WERE INITIALLY
bcftools view -S samples_order.txt merged.sex.bcf --output-type b --output {out_file_name}
'''
impute.command(cmd_order)
impute.command(f'bcftools index {out_file_name}')
impute.command(f'mv {out_file_name} {impute.ofile}')
impute.command(f'mv {out_file_name}.csi {impute.idx}')
b.write_output(
impute.ofile,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}'
)
b.write_output(
impute.idx,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}.csi'
)
# D. MIXED REGIONS
else:
if (start <= 2781479) & (end >= 2781479):
map_file_par = '/shapeit4/maps/b38/chrX_par1.b38.gmap.gz'
par_region = f'chrX:{start}-{2781479}'
non_par_region = f'chrX:{2781479}-{end}'
# to be used in step 3d
cmd_merge_regs = f'''
echo ORDERING PAR1 SAMPLES TO HOW THEY WERE INITIALLY
bcftools view -S samples_order.txt par.imputed.bcf --output-type b --output par.imputed.sort.bcf
bcftools index par.imputed.sort.bcf
rm par.imputed.bcf*
echo MERGING THE PAR1 AND NON-PAR FILES BACK TOGETHER
echo -e "par.imputed.sort.bcf\nnonpar.imputed.sort.bcf" > merge_regions.txt
bcftools concat --naive --file-list merge_regions.txt --output-type b --output {out_file_name}
'''
else:
map_file_par = '/shapeit4/maps/b38/chrX_par2.b38.gmap.gz'
if end > 156030895:
par_region = f'chrX:{155701383}-{156030895}'
else:
par_region = f'chrX:{155701383}-{end}'
non_par_region = f'chrX:{start}-{155701382}'
# to be used in step 3c
cmd_merge_regs = f'''
echo ORDERING PAR2 SAMPLES TO HOW THEY WERE INITIALLY
bcftools view -S samples_order.txt par.imputed.bcf --output-type b --output par.imputed.sort.bcf
bcftools index par.imputed.sort.bcf
rm par.imputed.bcf*
echo MERGING THE PAR2 AND NON-PAR FILES BACK TOGETHER
echo -e "nonpar.imputed.sort.bcf\npar.imputed.sort.bcf" > merge_regions.txt
bcftools concat --naive --file-list merge_regions.txt --output-type b --output {out_file_name}
'''
cmd_split = f'''
echo THIS CHUNK IS IN PAR1/2 and NON-PAR REGION, SO WE WILL SPLIT THESE TWO REGIONS
echo GETTING THE ORDER OF SAMPLES
bcftools query -l {vcf.bcf} > samples_order.txt
echo SPLITTING OUT THE PAR REGION
bcftools view {vcf.bcf} --regions {par_region} --output-type b --output par.bcf
echo SPLITTING OUT THE NON-PAR REGION
bcftools view {vcf.bcf} --regions {non_par_region} --output-type b --output nonpar.bcf
echo SPLITTING THE NON-PAR REGION BY SEX
bcftools view -S {in_females} nonpar.bcf --output-type b --output females.bcf
bcftools view -S ^{in_females} nonpar.bcf --output-type b --output males.bcf
echo INDEXING THE FILES BEFORE RUNNING IMPUTATION
bcftools index par.bcf
bcftools index females.bcf
bcftools index males.bcf
rm {vcf.bcf}
rm nonpar.bcf
'''
impute.command(cmd_split)
# (2) run imputation separately for par, females, and males
map_file = '/shapeit4/maps/b38/chrX.b38.gmap.gz'
cmd_impute = f'''
impute5_1.1.5_static --h {ref.bcf} --m {map_file_par} --g par.bcf --r {par_region} --out-gp-field \
--o par.imputed.bcf --b {buffer} --threads {threads}
impute5_1.1.5_static --h {ref.bcf} --m {map_file} --g females.bcf --r {non_par_region} --out-gp-field \
--o females.imputed.bcf --b {buffer} --threads {threads}
impute5_1.1.5_static --h {ref.bcf} --m {map_file} --g males.bcf --r {non_par_region} --out-gp-field \
--o males.imputed.bcf --b {buffer} --threads {threads} -- haploid
'''
impute.command(cmd_impute)
# (3) merge the imputed files back together into one chunk
# (3a) index females and males files to be merged and create a file with these for bcftools
cmd_index_chunks = f'''
bcftools index par.imputed.bcf
bcftools index females.imputed.bcf
bcftools index males.imputed.bcf
'''
impute.command(cmd_index_chunks)
# (3b) sometimes there are duplicates (raw and imputed with flipped alleles) and this causes an error when
# merging, so we remove any duplicates
# bcftools view Nepal_PTSD_GSA_Updated_May2021_qced.chrX.phased.bcf | grep "#"
cmd_sort = f'''
echo CHECKING FOR DUPLICATE VARIANTS AND REMOVING THEM
bcftools norm -d any females.imputed.bcf --output-type b --output females.imputed.sorted.bcf
rm females.imputed.bcf*
bcftools norm -d any males.imputed.bcf --output-type b --output males.imputed.sorted.bcf
rm males.imputed.bcf*
bcftools index females.imputed.sorted.bcf
bcftools index males.imputed.sorted.bcf
echo -e "females.imputed.sorted.bcf\nmales.imputed.sorted.bcf" > merge_sex.txt
'''
impute.command(cmd_sort)
# (3c) merge the sex files into one
cmd_merge_sex = f'''
echo MERGING THE MALES AND FEMALES FILE BACK TOGETHER
bcftools merge --file-list merge_sex.txt --output-type b --output nonpar.imputed.bcf
bcftools index nonpar.imputed.bcf
echo ORDERING NON-PAR SAMPLES TO HOW THEY WERE INITIALLY
bcftools view -S samples_order.txt nonpar.imputed.bcf --output-type b --output nonpar.imputed.sort.bcf
bcftools index nonpar.imputed.sort.bcf
rm nonpar.imputed.bcf* females.imputed.sorted.bcf* males.imputed.sorted.bcf
'''
impute.command(cmd_merge_sex)
# (3d) merge the non-par and par regions together
impute.command(cmd_merge_regs)
impute.command(f'bcftools index {out_file_name}')
impute.command(f'mv {out_file_name} {impute.ofile}')
impute.command(f'mv {out_file_name}.csi {impute.idx}')
b.write_output(
impute.ofile,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}'
)
b.write_output(
impute.idx,
f'{out_dir}/GWASpy/{file_dir}/Imputation/imputed_chunks/{out_file_name}.csi'
)
def concat_vcfs(b: hb.batch.Batch,
vcf_basename: str = None,
vcfs_to_merge: List = None,
output_type: str = 'bcf',
software: str = None,
chrom: str = None,
docker_img: str = 'docker.io/lindonkambule/gwaspy:v1',
cpu: int = 8,
out_dir: str = None):
global index_cmd
out_type = 'b' if output_type == 'bcf' else 'z'
threads = cpu - 1
vcfs_sizes_sum = 0
merge_vcf_i = ''
out_filename = f'{vcf_basename}.{chrom}.phased.{software}.bcf' if output_type == 'bcf' else \
f'{vcf_basename}.{chrom}.phased.{software}.vcf.gz'
out_index_name = f'{vcf_basename}.{chrom}.phased.{software}.bcf.csi' if output_type == 'bcf' else \
f'{vcf_basename}.{chrom}.phased.{software}.vcf.gz.csi'
for line in vcfs_to_merge:
vcfs_sizes_sum += 1 + bytes_to_gb(line)
mem = 'highmem' if vcfs_sizes_sum > 2 else 'standard'
disk_size = 10 + vcfs_sizes_sum
concat = b.new_job(name=f'concat-{vcf_basename}')
concat.memory(mem)
concat.storage(f'{disk_size}Gi')
concat.image(docker_img)
concat.cpu(cpu)
for line in vcfs_to_merge:
input_vcf = b.read_input_group(vcf=line, ind=f'{line}.csi')
merge_vcf_i += f'{input_vcf.vcf} '
cmd = f'''
bcftools concat \
--no-version \
--output-type {out_type} \
--output {out_filename} \
--threads {threads} \
--ligate \
{merge_vcf_i}
'''
concat.command(cmd)
# index the merged output
concat.command(f'bcftools index {out_filename}')
concat.command(f'mv {out_filename} {concat.ofile}')
concat.command(f'mv {out_index_name} {concat.idx}')
b.write_output(
concat.ofile,
f'{out_dir}/GWASpy/{vcf_basename}/Phasing/phased_merged/{out_filename}'
)
b.write_output(
concat.idx,
f'{out_dir}/GWASpy/{vcf_basename}/Phasing/phased_merged/{out_index_name}'
)