def variantcall_sample(data, region=None, out_file=None):
"""Parallel entry point for doing genotyping of a region of a sample.
"""
from bcbio.variation import freebayes, cortex, samtools, varscan, mutect
safe_makedir(os.path.dirname(out_file))
caller_fns = {"gatk": unified_genotyper,
"gatk-haplotype": haplotype_caller,
"freebayes": freebayes.run_freebayes,
"cortex": cortex.run_cortex,
"samtools": samtools.run_samtools,
"varscan": varscan.run_varscan,
"mutect": mutect.mutect_caller}
sam_ref = data["sam_ref"]
config = data["config"]
caller_fn = caller_fns[config["algorithm"].get("variantcaller", "gatk")]
if isinstance(data["work_bam"], basestring):
align_bams = [data["work_bam"]]
items = [data]
else:
align_bams = data["work_bam"]
items = data["work_items"]
call_file = "%s-raw%s" % os.path.splitext(out_file)
caller_fn(align_bams, items, sam_ref,
configured_vrn_files(config, sam_ref),
region, call_file)
if data["config"]["algorithm"].get("phasing", False) == "gatk":
call_file = phasing.read_backed_phasing(call_file, align_bams, sam_ref, region, config)
for ext in ["", ".idx"]:
if not os.path.exists(out_file + ext):
if os.path.exists(call_file + ext):
try:
os.symlink(call_file + ext, out_file + ext)
except OSError, msg:
if str(msg).find("File exists") == -1:
raise
def variantcall_sample(data, region=None, out_file=None):
"""Parallel entry point for doing genotyping of a region of a sample.
"""
safe_makedir(os.path.dirname(out_file))
sam_ref = data["sam_ref"]
config = data["config"]
caller_fns = get_variantcallers()
caller_fn = caller_fns[config["algorithm"].get("variantcaller", "gatk")]
if isinstance(data["work_bam"], basestring):
align_bams = [data["work_bam"]]
items = [data]
else:
align_bams = data["work_bam"]
items = data["work_items"]
call_file = "%s-raw%s" % os.path.splitext(out_file)
call_file = caller_fn(align_bams, items, sam_ref,
configured_vrn_files(config, sam_ref),
region, call_file)
if data["config"]["algorithm"].get("phasing", False) == "gatk":
call_file = phasing.read_backed_phasing(call_file, align_bams, sam_ref, region, config)
for ext in ["", ".idx"]:
if not os.path.exists(out_file + ext):
if os.path.exists(call_file + ext):
try:
os.symlink(call_file + ext, out_file + ext)
except OSError, msg:
if str(msg).find("File exists") == -1:
raise
def finalize_genotyper(call_file, ref_file, config):
"""Perform SNP genotyping and analysis using GATK.
"""
vrn_files = configured_vrn_files(config, ref_file)
filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
_eval_genotyper(filter_snp, ref_file, vrn_files.dbsnp, config)
return filter_snp
def finalize_genotyper(call_file, bam_file, ref_file, config):
"""Perform SNP genotyping and analysis.
"""
vrn_files = configured_vrn_files(config, ref_file)
variantcaller = config["algorithm"].get("variantcaller", "gatk")
if variantcaller in ["freebayes", "cortex", "samtools", "gatk-haplotype", "varscan"]:
call_file = annotation.annotate_nongatk_vcf(call_file, bam_file, vrn_files.dbsnp,
ref_file, config)
filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
return filter_snp
def finalize_genotyper(call_file, bam_file, ref_file, config):
"""Perform SNP genotyping and analysis.
"""
vrn_files = configured_vrn_files(config, ref_file)
variantcaller = config["algorithm"].get("variantcaller", "gatk")
if variantcaller in ["freebayes", "cortex"]:
call_file = freebayes.postcall_annotate(call_file, ref_file, vrn_files, config)
filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
phase_snp = phasing.read_backed_phasing(filter_snp, bam_file, ref_file, config)
_eval_genotyper(phase_snp, ref_file, vrn_files.dbsnp, config)
return phase_snp
def finalize_genotyper(call_file, bam_file, ref_file, config):
"""Perform SNP genotyping and analysis.
"""
vrn_files = configured_vrn_files(config, ref_file)
variantcaller = config["algorithm"].get("variantcaller", "gatk")
if variantcaller in ["freebayes", "cortex", "samtools"]:
call_file = freebayes.postcall_annotate(call_file, ref_file, vrn_files, config)
filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
phase_snp = phasing.read_backed_phasing(filter_snp, bam_file, ref_file, config)
_eval_genotyper(phase_snp, ref_file, vrn_files.dbsnp, config)
return phase_snp
def postprocess_variants(data):
"""Provide post-processing of variant calls: filtering and effects annotation.
"""
logger.info("Finalizing variant calls: %s" % str(data["name"]))
if data["work_bam"] and data.get("vrn_file"):
vrn_files = configured_vrn_files(data["config"], data["sam_ref"])
data["vrn_file"] = variant_filtration(data["vrn_file"], data["sam_ref"], vrn_files,
data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file = effects.snpeff_effects(data)
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
return [[data]]
def finalize_genotyper(call_file, bam_file, ref_file, config):
"""Perform SNP genotyping and analysis.
"""
vrn_files = configured_vrn_files(config, ref_file)
variantcaller = config["algorithm"].get("variantcaller", "gatk")
if variantcaller in [
"freebayes", "cortex", "samtools", "gatk-haplotype", "varscan"
]:
call_file = annotation.annotate_nongatk_vcf(call_file, bam_file,
vrn_files.dbsnp, ref_file,
config)
filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
return filter_snp
def variantcall_sample(data, region=None, out_file=None):
"""Parallel entry point for doing genotyping of a region of a sample.
"""
from bcbio.variation import freebayes, cortex, samtools, varscan, mutect
safe_makedir(os.path.dirname(out_file))
caller_fns = {
"gatk": unified_genotyper,
"gatk-haplotype": haplotype_caller,
"freebayes": freebayes.run_freebayes,
"cortex": cortex.run_cortex,
"samtools": samtools.run_samtools,
"varscan": varscan.run_varscan,
"mutect": mutect.mutect_caller
}
sam_ref = data["sam_ref"]
config = data["config"]
caller_fn = caller_fns[config["algorithm"].get("variantcaller", "gatk")]
if isinstance(data["work_bam"], basestring):
align_bams = [data["work_bam"]]
items = [data]
else:
align_bams = data["work_bam"]
items = data["work_items"]
call_file = "%s-raw%s" % os.path.splitext(out_file)
caller_fn(align_bams, items, sam_ref,
configured_vrn_files(config, sam_ref), region, call_file)
if data["config"]["algorithm"].get("phasing", False) == "gatk":
call_file = phasing.read_backed_phasing(call_file, align_bams, sam_ref,
region, config)
for ext in ["", ".idx"]:
if not os.path.exists(out_file + ext):
if os.path.exists(call_file + ext):
try:
os.symlink(call_file + ext, out_file + ext)
except OSError, msg:
if str(msg).find("File exists") == -1:
raise
