def concatenate_vcfs(in_vcfs, in_chrom, out_vcf, out_log):
args = locals()
default = {
'main_script':
pkg_resources.resource_filename(
'yaps2',
'resources/postvqsr38/concatenate-partitioned-chromosome-vcfs.sh'),
}
cmd_args = merge_params(default, args)
cmd = None
if len(cmd_args['in_vcfs']) == 1:
cmd_args['in_vcfs'] = cmd_args['in_vcfs'][0]
cmd = ("cp -v {in_vcfs} {out_vcf} "
">{out_log} "
"2>&1").format(**cmd_args)
else:
cmd_args['in_vcfs'] = ' '.join(
[x for x in in_vcfs if not empty_gzipped_vcf(x)])
cmd = ("{main_script} "
"-m {out_vcf} "
"{in_vcfs} "
">{out_log} "
"2>&1").format(**cmd_args)
return cmd
def gatk_select_variants_remove_ac_0(in_chrom, in_vcf, out_vcf, out_log):
args = locals()
default = {
'java':
'/gapp/x64linux/opt/java/jre/jre1.7.0_45/bin/java',
'jar':
'/usr/share/java/GenomeAnalysisTK-3.4.jar',
'java_opts':
"-Xmx4096m",
'reference':
'/gscmnt/gc2719/halllab/genomes/human/GRCh37/1kg_phase1/human_g1k_v37.fasta',
}
cmd_args = merge_params(default, args)
cmd = ("{java} -jar {jar} "
"-T SelectVariants -R {reference} "
"--removeUnusedAlternates "
"-V {in_vcf} "
"-L {in_chrom} "
"-o {out_vcf} "
">{out_log} "
"2>&1").format(**cmd_args)
return cmd
def bcftools_stats_summary(in_dir, out_dir):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/bcftools-stats-summary-plots.sh'),
}
cmd_args = merge_params(default, args)
cmd = "{script} {in_dir} {out_dir}".format(**cmd_args)
return cmd
def annotation_1000G(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/annotate-w-1000G.sh'),
}
cmd_args = merge_params(default, args)
cmd = "{script} {in_vcf} {out_vcf} >{out_log} 2>&1".format(**cmd_args)
return cmd
def variant_eval_summary(in_dir, out_dir):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2',
'resources/postvqsr/merge-and-plot-gatk-variant-eval-stats.sh'),
}
cmd_args = merge_params(default, args)
cmd = "{script} {in_dir} {out_dir}".format(**cmd_args)
return cmd
def filter_biallelic_snps(in_vcf, out_vcf, in_min_vqslod, **kwargs):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/pca/vcf-filter-biallelic-snps.sh'),
}
cmd_args = merge_params(default, args)
cmd = ("{script} {in_vcf} {out_vcf} {in_min_vqslod}").format(**cmd_args)
return cmd
def plink_binary(in_vcf, out_path, **kwargs):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/pca/create-plink-binary.sh'),
}
cmd_args = merge_params(default, args)
cmd = ("{script} {in_vcf} {out_path}").format(**cmd_args)
return cmd
def plink_ld_prune(in_path, out_path, **kwargs):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/pca/plink-ld-prune.sh'),
}
cmd_args = merge_params(default, args)
cmd = ("{script} {in_path} {out_path}").format(**cmd_args)
return cmd
def plink_merge_pruned_files(in_ref, in_merge_file, out_path):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/pca/plink-merge-pruned.sh'),
}
cmd_args = merge_params(default, args)
cmd = ("{script} {in_ref} {in_merge_file} {out_path}").format(**cmd_args)
return cmd
def normalize_decompose_unique(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename('yaps2',
'resources/postvqsr/run-decompose.sh'),
}
cmd_args = merge_params(default, args)
cmd = "{script} {in_vcf} {out_vcf} {in_chrom} >{out_log} 2>&1".format(
**cmd_args)
return cmd
def remove_symbolic_deletion_alleles(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/remove-symbolic.sh'),
}
cmd_args = merge_params(default, args)
cmd = "{script} {in_vcf} {out_vcf} >{out_log} 2>&1".format(**cmd_args)
return cmd
def annotation_vep(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'main_script':
pkg_resources.resource_filename('yaps2',
'resources/postvqsr38/run-vep.sh'),
}
cmd_args = merge_params(default, args)
cmd = ("{main_script} "
"{in_vcf} "
"{out_vcf} "
">{out_log} 2>&1").format(**cmd_args)
return cmd
def count_sample_missingness(in_vcf, in_chrom, out_json, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/count-sample-missingness.py'),
'python':
sys.executable,
}
cmd_args = merge_params(default, args)
cmd = "{python} {script} --out={out_json} {in_vcf} >{out_log} 2>&1".format(
**cmd_args)
return cmd
def create_evec_data_frame(in_file, out_file):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/pca/make-pca-evec-data-frame.py'),
}
cmd_args = merge_params(default, args)
cmd = ( "python -u {script} "
"--src={in_file} "
"--out={out_file} ").format(**cmd_args)
return cmd
def eigenstrat_smartpca_analysis(in_ped_file, in_map_file, out_prj_dir):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/pca/eigenstrat.mk'),
}
cmd_args = merge_params(default, args)
cmd = ( "make -f {script} "
"INPUT_PED={in_ped_file} "
"INPUT_MAP={in_map_file} "
"PRJ_DIR={out_prj_dir}" ).format(**cmd_args)
return cmd
def annotation_vep_cadd(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'main_script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/vep-cadd-annotation.sh'),
'merge_script':
pkg_resources.resource_filename('yaps2',
'resources/postvqsr/merge-in-cadd.py'),
}
cmd_args = merge_params(default, args)
cmd = "{main_script} {in_vcf} {out_vcf} {merge_script} >{out_log} 2>&1".format(
**cmd_args)
return cmd
def calculate_sample_missingness(in_json, out_stats, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2',
'resources/postvqsr38/calculate-overall-sample-missingness.py'),
'python':
sys.executable,
}
cmd_args = merge_params(default, args)
cmd = "{python} {script} --out={out_stats} {in_json} >{out_log} 2>&1".format(
**cmd_args)
return cmd
def plink_pipeline(in_vcf, in_trio_fam, out_dir, **kwargs):
args = locals()
default = {
'script':
pkg_resources.resource_filename('yaps2', 'resources/mie/plink.mk'),
}
cmd_args = merge_params(default, args)
cmd = ("make -f {script} "
"INPUT_VCF={in_vcf} "
"TRIO_FAM={in_trio_fam} "
"PRJ_DIR={out_dir}").format(**cmd_args)
return cmd
def exec_speedseq(output_prefix, tmpdir, input_bams, **kwargs):
args = locals()
default = {
'script' : pkg_resources.resource_filename('yaps2', 'resources/b38/speedseq-realign.sh'),
# build 38
'reference' : os.path.join(
'/gscmnt/gc2802/halllab/ccdg_resources/genomes',
'human/GRCh38DH/bwa/0_7_12/all_sequences.fa'
),
}
cmd_args = merge_params(default, args)
cmd = ("{script} {output_prefix} {tmpdir} {reference} {input_bams}").format(**cmd_args)
return cmd
def aggregate_mie_statistics(in_category, in_method, in_dir, out_file):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/mie/aggregate-mie-statistics.py'),
}
cmd_args = merge_params(default, args)
cmd = ("{script} "
"--input-dir={in_dir} "
"--output-file={out_file} "
"--category={in_category} "
"--method={in_method}").format(**cmd_args)
return cmd
def annotation_LINSIGHT(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'main_script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr38/annotate-w-LINSIGHT.sh'),
'b37_to_b38_integration_script':
pkg_resources.resource_filename(
'yaps2',
'resources/postvqsr38/integrate-b37-annotations-to-b38.py'),
}
cmd_args = merge_params(default, args)
cmd = ("{main_script} "
"{in_vcf} "
"{out_vcf} "
"{b37_to_b38_integration_script} "
">{out_log} 2>&1").format(**cmd_args)
return cmd
def vcf_partition(in_vcf, out_vcf, in_min_vqslod, in_max_vqslod, in_samples,
in_type, in_method, in_chrom, in_label):
args = locals()
default = {
'script':
pkg_resources.resource_filename('yaps2',
'resources/mie/vcf-partition.sh'),
}
cmd_args = merge_params(default, args)
cmd = ("{script} {in_vcf} {out_vcf} "
"{in_min_vqslod} "
"{in_max_vqslod} "
"{in_samples} "
"{in_type} "
"{in_method}").format(**cmd_args)
return cmd
def annotate_allele_balances(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/allele-balance-annotation.sh'),
'python_script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/annotate-allele-balances.py'),
'python_executable':
sys.executable,
}
cmd_args = merge_params(default, args)
cmd = ("{script} "
"{python_executable} {python_script} "
"{in_vcf} {out_vcf} {in_chrom} "
">{out_log} 2>&1").format(**cmd_args)
return cmd
def bcftools_stats(in_vcf, in_chrom, out_stats):
args = locals()
default = {
'bcftools':
'/gscmnt/gc2802/halllab/idas/software/local/bin/bcftools1.4',
'reference':
'/gscmnt/ams1102/info/model_data/2869585698/build106942997/all_sequences.fa',
}
cmd_args = merge_params(default, args)
cmd = ("{bcftools} stats "
"--split-by-ID "
"-F {reference} "
"-s - "
"-f '.,PASS' "
"{in_vcf} "
">{out_stats}").format(**cmd_args)
return cmd
def bcftools_stats(in_vcf, in_chrom, out_stats):
args = locals()
default = {
'bcftools':
'/gscmnt/gc2802/halllab/idas/software/local/bin/bcftools1.4',
'reference':
'/gscmnt/gc2802/halllab/ccdg_resources/genomes/human/GRCh38DH/all_sequences.fa',
}
cmd_args = merge_params(default, args)
cmd = ("{bcftools} stats "
"--split-by-ID "
"-F {reference} "
"-s - "
"-f '.,PASS' "
"{in_vcf} "
">{out_stats}").format(**cmd_args)
return cmd
def gatk_variant_eval(in_chrom, in_vcf, out_stats, out_log):
args = locals()
default = {
'java':
'/gapp/x64linux/opt/java/jre/jre1.8.0_31/bin/java',
'jar':
'/gscmnt/gc2802/halllab/idas/jira/BIO-1662/vendor/local/jars/GenomeAnalysisTK-3.5-idas-experimental-293f64d-2016.02.19.jar',
'java_opts':
"-Xmx4096m",
'reference':
'/gscmnt/gc2719/halllab/genomes/human/GRCh37/1kg_phase1/human_g1k_v37.fasta',
'dbsnp':
'/gscmnt/gc2802/halllab/idas/jira/BIO-1662/data/derived/FinnMetSeq-WGS/10-decompose-normalize-1000G-variant-ref-v1/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.decompose.normalize.vcf.gz',
}
cmd_args = merge_params(default, args)
cmd = ("{java} -jar {jar} "
"-nt 8 "
"-T VariantEval "
"-D {dbsnp} "
"-R {reference} "
"-ST Sample "
"-noST "
"-EV TiTvVariantEvaluator "
"-EV CountVariants "
"-EV CompOverlap "
"-EV IndelSummary "
"-EV MultiallelicSummary "
"-noEV "
"-L {in_chrom} "
"-eval {in_vcf} "
"-o {out_stats} "
">{out_log} "
"2>&1").format(**cmd_args)
return cmd
def filter_variant_missingness(in_vcf, in_chrom, out_vcf, out_log):
args = locals()
default = {
'script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/filter-missingness-sites.sh'),
'python_script':
pkg_resources.resource_filename(
'yaps2', 'resources/postvqsr/filter-site-missingness.py'),
'python_executable':
sys.executable,
}
cmd_args = merge_params(default, args)
if in_chrom.startswith('Y') or in_chrom.startswith('y'):
cmd_args['out_vcf'] = os.path.dirname(out_vcf)
cmd = "/bin/cp -v {in_vcf}* {out_vcf} >{out_log} 2>&1".format(
**cmd_args)
else:
cmd = ("{script} "
"{python_executable} {python_script} "
"{in_vcf} {out_vcf} {in_chrom} "
">{out_log} 2>&1").format(**cmd_args)
return cmd
def concatenate_vcfs(in_vcfs, in_chrom, out_vcf, out_log):
args = locals()
default = {
'bcftools':
'/gscmnt/gc2802/halllab/idas/software/local/bin/bcftools1.4',
}
cmd_args = merge_params(default, args)
cmd = None
if len(cmd_args['in_vcfs']) == 1:
cmd_args['in_vcfs'] = cmd_args['in_vcfs'][0]
cmd = ("cp -v {in_vcfs} {out_vcf}"
">{out_log} "
"2>&1").format(**cmd_args)
else:
cmd_args['in_vcfs'] = ' '.join(
[x for x in in_vcfs if not empty_gzipped_vcf(x)])
cmd = ("{bcftools} concat "
"-a "
"{in_vcfs} "
"-O z -o {out_vcf}"
">{out_log} "
"2>&1").format(**cmd_args)
return cmd
