def add_or_replace_read_groups(input_sam, sorted_bam, completed_file):
"""
Picard Tools - AddOrReplaceReadGroups.
Places each read into a read group for GATK processing. Really only
informative if there are multiple samples.
"""
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['picardtools'],
'AddOrReplaceReadGroups',
'INPUT=' + input_sam,
'OUTPUT=' + sorted_bam,
'SORT_ORDER=coordinate',
'RGID=GATK',
'RGLB=GATK',
'RGPL=Illumina',
'RGSM=GATK',
'RGPU=GATK',
'VALIDATION_STRINGENCY=LENIENT'
])
if shared.try_to_complete_task(sorted_bam, completed_file):
return True
else:
raise Exception("AddOrReplaceReadGroups didn't complete successfully.")
def create_sequence_dictionary(reference, output):
""" Index the reference FASTA file. """
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['picardtools'],
'CreateSequenceDictionary',
'REFERENCE=' + reference,
'OUTPUT=' + output,
])
def copy_vcf(filtered_vcf, annotated_vcf, completed_file):
""" Annotate called SNPs/InDel. """
shared.run_command(
['cp', filtered_vcf, annotated_vcf],
)
if shared.try_to_complete_task(annotated_vcf, completed_file):
return True
else:
raise Exception("Could not copy filtered VCF successfully.")
def bwa_mem(fastq, output_sam, num_cpu, reference, completed_file):
""" Align reads (mean length < 70bp) against reference genome. """
shared.run_command(
[BIN['bwa'], 'mem', '-M', '-t', num_cpu, reference, fastq],
stdout=output_sam
)
if shared.try_to_complete_task(output_sam, completed_file):
return True
else:
raise Exception("bwa mem did not complete successfully.")
def move_final_vcf(annotated_vcf, compressed_vcf, completed_file):
""" Move the final VCF to the project root. """
shared.run_command(
['gzip', '-c', annotated_vcf],
stdout=compressed_vcf
)
if shared.try_to_complete_task(compressed_vcf, completed_file):
return True
else:
raise Exception("final vcf gzip did not complete successfully.")
def vcf_annotator(filtered_vcf, annotated_vcf, genbank, completed_file):
""" Annotate called SNPs/InDel. """
shared.run_command(
[BIN['vcf_annotator'],
'--gb', genbank,
'--vcf', filtered_vcf],
stdout=annotated_vcf
)
if shared.try_to_complete_task(annotated_vcf, completed_file):
return True
else:
raise Exception("vcf-annotator did not complete successfully.")
def bwa_aln(fastq, sai, output_sam, num_cpu, reference, completed_file):
""" Align reads (mean length < 70bp) against reference genome. """
shared.run_command([
BIN['bwa'], 'aln', '-f', sai, '-t', num_cpu, reference, fastq
])
shared.run_command([
BIN['bwa'], 'samse', '-f', output_sam, reference, sai, fastq
])
if shared.try_to_complete_task(output_sam, completed_file):
return True
else:
raise Exception("bwa aln/samse did not complete successfully.")
def indel_realigner(intervals, deduped_bam, realigned_bam, reference,
completed_file):
"""
GATK Best Practices - Realign Indels.
GATK - IndelRealigner: Realign InDel regions.
"""
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['gatk'],
'-T', 'IndelRealigner',
'-R', reference,
'-I', deduped_bam,
'-o', realigned_bam,
'-targetIntervals', intervals
])
if shared.try_to_complete_task(realigned_bam, completed_file):
return True
else:
raise Exception("IndelRealigner did not complete successfully.")
def realigner_target_creator(deduped_bam, intervals, reference,
completed_file):
"""
GATK Best Practices - Realign Indels.
GATK - RealignerTargetCreator: Create a list of InDel regions to be
realigned.
"""
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['gatk'],
'-T', 'RealignerTargetCreator',
'-R', reference,
'-I', deduped_bam,
'-o', intervals
])
if shared.try_to_complete_task(intervals, completed_file):
return True
else:
raise Exception("RealignerTargetCreator didn't complete successfully.")
def variant_filtration(input_vcf, filtered_vcf, reference, completed_file):
""" Apply filters to the input VCF. """
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['gatk'],
'-T', 'VariantFiltration',
'-R', reference,
'-V', input_vcf,
'-o', filtered_vcf,
'--clusterSize', '3',
'--clusterWindowSize', '10',
'--filterExpression', 'DP < 9 && AF < 0.7',
'--filterName', 'Fail',
'--filterExpression', 'DP > 9 && AF >= 0.95',
'--filterName', 'SuperPass',
'--filterExpression', 'GQ < 20',
'--filterName', 'LowGQ'
])
if shared.try_to_complete_task(filtered_vcf, completed_file):
return True
else:
raise Exception("VariantFiltration did not complete successfully.")
def mark_duplicates(sorted_bam, deduped_bam, completed_file):
"""
GATK Best Practices - Mark Duplicates.
Picard Tools - MarkDuplicates: Remove mark identical reads as duplicates
for GATK to ignore.
"""
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['picardtools'],
'MarkDuplicates',
'INPUT=' + sorted_bam,
'OUTPUT=' + deduped_bam,
'METRICS_FILE=' + deduped_bam + '_metrics',
'ASSUME_SORTED=true',
'REMOVE_DUPLICATES=false',
'VALIDATION_STRINGENCY=LENIENT'
])
if shared.try_to_complete_task(deduped_bam, completed_file):
build_bam_index(deduped_bam)
return True
else:
raise Exception("MarkDuplicates didn't complete successfully.")
def haplotype_caller(realigned_bam, output_vcf, num_cpu, reference,
completed_file):
"""
GATK Best Practices - Call Variants.
GATK - HaplotypeCaller: Call variants (SNPs and InDels)
"""
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['gatk'],
'-T', 'HaplotypeCaller',
'-R', reference,
'-I', realigned_bam,
'-o', output_vcf,
'-ploidy', '1',
'-stand_call_conf', '30.0',
'-stand_emit_conf', '10.0',
'-rf', 'BadCigar',
'-nct', num_cpu
])
if shared.try_to_complete_task(output_vcf, completed_file):
return True
else:
raise Exception("HaplotypeCaller did not complete successfully.")
def bwa_index(fasta):
""" Create a BWA index. """
shared.run_command(
[BIN['bwa'], 'index', fasta],
)
def samtools_faidx(fasta):
""" Index the reference FASTA file. """
shared.run_command(
[BIN['samtools'], 'faidx', fasta],
)
def build_bam_index(bam):
shared.run_command([
BIN['java'], '-Xmx8g', '-jar', BIN['picardtools'],
'BuildBamIndex',
'INPUT=' + bam,
])