def genotype_filter(vcf_file, expression, data, name, filterext=""):
"""Perform genotype based filtering using GATK with the provided expression.
Adds FT tags to genotypes, rather than the general FILTER flag.
"""
base, ext = utils.splitext_plus(vcf_file)
out_file = "{base}-filter{filterext}{ext}".format(**locals())
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
params = [
"-T",
"VariantFiltration",
"-R",
tz.get_in(["reference", "fasta", "base"], data),
"--variant",
vcf_file,
"--out",
tx_out_file,
"--genotypeFilterName",
name,
"--genotypeFilterExpression",
"'%s'" % expression,
]
jvm_opts = broad.get_gatk_framework_opts(data["config"])
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter with expression: %s" % expression)
if out_file.endswith(".vcf.gz"):
out_file = vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
def gatk_filter_rnaseq(vrn_file, data):
"""
this incorporates filters listed here, dropping clusters of variants
within a 35 nucleotide window, high fischer strand values and low
quality by depth
https://software.broadinstitute.org/gatk/guide/article?id=3891
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V
input.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0"
-filterName QD -filter "QD < 2.0" -o output.vcf
"""
out_file = "%s-filter%s" % utils.splitext_plus(vrn_file)
if not file_exists(out_file):
ref_file = dd.get_ref_file(data)
with file_transaction(data, out_file) as tx_out_file:
params = [
"VariantFiltration", "-R", ref_file, "-V", vrn_file,
"--cluster-window-size", "35", "--cluster-size", "3",
"--filter-expression", "'FS > 30.0'", "--filter-name", "FS",
"--filter-expression", "'QD < 2.0'", "--filter-name", "QD",
"--output", tx_out_file
]
# Use GATK4 for filtering, tools_off is for variant calling
config = utils.deepish_copy(dd.get_config(data))
if "gatk4" in dd.get_tools_off({"config": config}):
config["algorithm"]["tools_off"].remove("gatk4")
jvm_opts = broad.get_gatk_opts(config,
os.path.dirname(tx_out_file))
do.run(broad.gatk_cmd("gatk", jvm_opts, params, config),
"Filter RNA-seq variants.")
return out_file
def gatk_filter_rnaseq(vrn_file, data):
"""
this incorporates filters listed here, dropping clusters of variants
within a 35 nucleotide window, high fischer strand values and low
quality by depth
https://software.broadinstitute.org/gatk/guide/article?id=3891
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V
input.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0"
-filterName QD -filter "QD < 2.0" -o output.vcf
"""
out_file = "%s-filter%s" % utils.splitext_plus(vrn_file)
if not file_exists(out_file):
ref_file = dd.get_ref_file(data)
with file_transaction(data, out_file) as tx_out_file:
params = ["VariantFiltration",
"-R", ref_file,
"-V", vrn_file,
"--cluster-window-size", "35",
"--cluster-size", "3",
"--filter-expression", "'FS > 30.0'",
"--filter-name", "FS",
"--filter-expression", "'QD < 2.0'",
"--filter-name", "QD",
"--output", tx_out_file]
# Use GATK4 for filtering, tools_off is for variant calling
config = utils.deepish_copy(dd.get_config(data))
if "gatk4" in dd.get_tools_off({"config": config}):
config["algorithm"]["tools_off"].remove("gatk4")
jvm_opts = broad.get_gatk_opts(config, os.path.dirname(tx_out_file))
do.run(broad.gatk_cmd("gatk", jvm_opts, params, config), "Filter RNA-seq variants.")
return out_file
def gatk_filter_rnaseq(vrn_file, data):
"""
this incorporates filters listed here, dropping clusters of variants
within a 35 nucleotide window, high fischer strand values and low
quality by depth
https://software.broadinstitute.org/gatk/guide/article?id=3891
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V
input.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0"
-filterName QD -filter "QD < 2.0" -o output.vcf
"""
out_file = "%s-filter%s" % utils.splitext_plus(vrn_file)
if not file_exists(out_file):
ref_file = dd.get_ref_file(data)
with file_transaction(data, out_file) as tx_out_file:
params = ["-T", "VariantFiltration",
"-R", ref_file,
"-V", vrn_file,
"--clusterWindowSize", "35",
"--clusterSize", "3",
"--filterExpression", "\"'FS > 30.0'\"",
"--filterName", "FS",
"--filterExpression", "\"'QD < 2.0'\"",
"--filterName", "QD",
"-o", tx_out_file]
jvm_opts = broad.get_gatk_framework_opts(dd.get_config(data), os.path.dirname(tx_out_file))
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter RNA-seq variants.")
return out_file
def concat_variant_files_catvariants(orig_files, out_file, regions, ref_file, config):
"""Concatenate multiple variant files from regions into a single output file.
Uses GATK CatVariants as a lightweight approach to merging VCF files split
by regions with the same sample information, so no complex merging needed.
Handles both plain text and bgzipped/tabix indexed outputs.
Falls back to bcftools concat if fails due to GATK stringency issues.
"""
if not utils.file_exists(out_file):
input_file_list = _get_file_list(orig_files, out_file, regions, ref_file, config)
failed = False
with file_transaction(config, out_file) as tx_out_file:
params = ["org.broadinstitute.gatk.tools.CatVariants",
"-R", ref_file,
"-V", input_file_list,
"-out", tx_out_file,
"-assumeSorted"]
jvm_opts = broad.get_gatk_framework_opts(config, os.path.dirname(tx_out_file), include_gatk=False)
try:
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Concat variant files", log_error=False)
except subprocess.CalledProcessError as msg:
if ("We require all VCFs to have complete VCF headers" in str(msg) or
"Features added out of order" in str(msg) or
"The reference allele cannot be missing" in str(msg)):
os.remove(tx_out_file)
failed = True
else:
raise
if failed:
return _run_concat_variant_files_bcftools(input_file_list, out_file, config)
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
return out_file
def gatk_filter_rnaseq(data, vrn_file, out_file):
"""
this incorporates filters listed here, dropping clusters of variants
within a 35 nucleotide window, high fischer strand values and low
quality by depth
https://software.broadinstitute.org/gatk/guide/article?id=3891
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V
input.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0"
-filterName QD -filter "QD < 2.0" -o output.vcf
"""
broad_runner = broad.runner_from_config(dd.get_config(data))
ref_file = dd.get_ref_file(data)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tx_out_file:
params = ["-T", "VariantFiltration",
"-R", ref_file,
"-V", vrn_file,
"--clusterWindowSize", "35",
"--clusterSize", "3",
"--filterExpression", "\"'FS > 30.0'\"",
"--filterName", "FS",
"--filterExpression", "\"'QD < 2.0'\"",
"--filterName", "QD",
"-o", tx_out_file]
jvm_opts = broad.get_gatk_framework_opts(dd.get_config(data), os.path.dirname(tx_out_file))
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params),
"Filter variants.")
return out_file
def concat_variant_files_catvariants(orig_files, out_file, regions, ref_file, config):
"""Concatenate multiple variant files from regions into a single output file.
Uses GATK CatVariants as a lightweight approach to merging VCF files split
by regions with the same sample information, so no complex merging needed.
Handles both plain text and bgzipped/tabix indexed outputs.
Falls back to bcftools concat if fails due to GATK stringency issues.
"""
if not utils.file_exists(out_file):
input_file_list = _get_file_list(orig_files, out_file, regions, ref_file, config)
failed = False
with file_transaction(config, out_file) as tx_out_file:
params = ["org.broadinstitute.gatk.tools.CatVariants",
"-R", ref_file,
"-V", input_file_list,
"-out", tx_out_file,
"-assumeSorted"]
jvm_opts = broad.get_gatk_framework_opts(config, os.path.dirname(tx_out_file), include_gatk=False)
try:
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Concat variant files", log_error=False)
except subprocess.CalledProcessError as msg:
if ("We require all VCFs to have complete VCF headers" in str(msg) or
"Features added out of order" in str(msg) or
"The reference allele cannot be missing" in str(msg)):
os.remove(tx_out_file)
failed = True
else:
raise
if failed:
return _run_concat_variant_files_bcftools(input_file_list, out_file, config)
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
return out_file
def combine_variant_files(orig_files, out_file, ref_file, config,
quiet_out=True, region=None):
"""Combine VCF files from the same sample into a single output file.
Handles cases where we split files into SNPs/Indels for processing then
need to merge back into a final file.
Will parallelize up to 4 cores based on documented recommendations:
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/
org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php
"""
in_pipeline = False
if isinstance(orig_files, dict):
file_key = config["file_key"]
in_pipeline = True
orig_files = orig_files[file_key]
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
exist_files = [x for x in orig_files if os.path.exists(x)]
ready_files = run_multicore(p_bgzip_and_index, [[x, config] for x in exist_files], config)
params = ["-T", "CombineVariants",
"-R", ref_file,
"--out", tx_out_file]
priority_order = []
for i, ready_file in enumerate(ready_files):
name = "v%s" % i
params.extend(["--variant:{name}".format(name=name), ready_file])
priority_order.append(name)
params.extend(["--rod_priority_list", ",".join(priority_order)])
params.extend(["--genotypemergeoption", "PRIORITIZE"])
if quiet_out:
params.extend(["--suppressCommandLineHeader", "--setKey", "null"])
if region:
variant_regions = config["algorithm"].get("variant_regions", None)
cur_region = shared.subset_variant_regions(variant_regions, region, out_file)
if cur_region:
params += ["-L", bamprep.region_to_gatk(cur_region),
"--interval_set_rule", "INTERSECTION"]
cores = tz.get_in(["algorithm", "num_cores"], config, 1)
if cores > 1:
params += ["-nt", min(cores, 4)]
memscale = {"magnitude": 0.9 * cores, "direction": "increase"} if cores > 1 else None
jvm_opts = broad.get_gatk_framework_opts(config, os.path.dirname(tx_out_file), memscale=memscale,
parallel_gc=True)
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Combine variant files")
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
if in_pipeline:
return [{file_key: out_file, "region": region, "sam_ref": ref_file, "config": config}]
else:
return out_file
def concat_variant_files(orig_files, out_file, regions, ref_file, config):
"""Concatenate multiple variant files from regions into a single output file.
Lightweight approach to merging VCF files split by regions with the same
sample information, so no complex merging needed. Handles both plain text
and bgzipped/tabix indexed outputs.
Falls back to bcftools concat if fails due to GATK stringency issues.
"""
if not utils.file_exists(out_file):
sorted_files = _sort_by_region(orig_files, regions, ref_file, config)
exist_files = [
x for x in sorted_files
if os.path.exists(x) and vcf_has_variants(x)
]
if len(exist_files) == 0: # no non-empty inputs, merge the empty ones
exist_files = [x for x in sorted_files if os.path.exists(x)]
ready_files = run_multicore(p_bgzip_and_index,
[[x, config] for x in exist_files], config)
input_file_list = "%s-files.list" % utils.splitext_plus(out_file)[0]
with open(input_file_list, "w") as out_handle:
for fname in ready_files:
out_handle.write(fname + "\n")
failed = False
with file_transaction(config, out_file) as tx_out_file:
params = [
"org.broadinstitute.gatk.tools.CatVariants", "-R", ref_file,
"-V", input_file_list, "-out", tx_out_file, "-assumeSorted"
]
jvm_opts = broad.get_gatk_framework_opts(
config, os.path.dirname(tx_out_file), include_gatk=False)
try:
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params),
"Concat variant files",
log_error=False)
except subprocess.CalledProcessError as msg:
if ("We require all VCFs to have complete VCF headers"
in str(msg)
or "Features added out of order" in str(msg) or
"The reference allele cannot be missing" in str(msg)):
os.remove(tx_out_file)
failed = True
else:
raise
if failed:
return _run_concat_variant_files_bcftools(input_file_list,
out_file, config)
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
return out_file
def combine_variant_files(orig_files, out_file, ref_file, config,
quiet_out=True, region=None):
"""Combine VCF files from the same sample into a single output file.
Handles cases where we split files into SNPs/Indels for processing then
need to merge back into a final file.
Will parallelize up to 4 cores based on documented recommendations:
https://www.broadinstitute.org/gatk/gatkdocs/
org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php
"""
in_pipeline = False
if isinstance(orig_files, dict):
file_key = config["file_key"]
in_pipeline = True
orig_files = orig_files[file_key]
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
exist_files = [x for x in orig_files if os.path.exists(x)]
ready_files = run_multicore(p_bgzip_and_index, [[x, config] for x in exist_files], config)
params = ["-T", "CombineVariants",
"-R", ref_file,
"--out", tx_out_file]
priority_order = []
for i, ready_file in enumerate(ready_files):
name = "v%s" % i
params.extend(["--variant:{name}".format(name=name), ready_file])
priority_order.append(name)
params.extend(["--rod_priority_list", ",".join(priority_order)])
params.extend(["--genotypemergeoption", "PRIORITIZE"])
if quiet_out:
params.extend(["--suppressCommandLineHeader", "--setKey", "null"])
if region:
variant_regions = config["algorithm"].get("variant_regions", None)
cur_region = shared.subset_variant_regions(variant_regions, region, out_file)
if cur_region:
params += ["-L", bamprep.region_to_gatk(cur_region),
"--interval_set_rule", "INTERSECTION"]
cores = tz.get_in(["algorithm", "num_cores"], config, 1)
if cores > 1:
params += ["-nt", min(cores, 4)]
memscale = {"magnitude": 0.9 * cores, "direction": "increase"} if cores > 1 else None
jvm_opts = broad.get_gatk_framework_opts(config, memscale=memscale)
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Combine variant files")
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
if in_pipeline:
return [{file_key: out_file, "region": region, "sam_ref": ref_file, "config": config}]
else:
return out_file
def _gatk_extract_reads_cl(data, region, prep_params, tmp_dir):
"""Use GATK to extract reads from full BAM file.
"""
requires_gatkfull = False
args = ["-T", "PrintReads",
"-L", region_to_gatk(region),
"-R", dd.get_ref_file(data),
"-I", data["work_bam"]]
if requires_gatkfull:
runner = broad.runner_from_config(data["config"])
return runner.cl_gatk(args, tmp_dir)
else:
jvm_opts = broad.get_gatk_framework_opts(data["config"], tmp_dir)
return broad.gatk_cmd("gatk-framework", jvm_opts, args)
def _gatk_extract_reads_cl(data, region, prep_params, tmp_dir):
"""Use GATK to extract reads from full BAM file, recalibrating if configured.
"""
requires_gatkfull = False
args = ["-T", "PrintReads", "-L", region_to_gatk(region), "-R", data["sam_ref"], "-I", data["work_bam"]]
if prep_params["recal"] == "gatk":
if "prep_recal" in data and _recal_has_reads(data["prep_recal"]):
requires_gatkfull = True
args += ["-BQSR", data["prep_recal"]]
elif prep_params["recal"]:
raise NotImplementedError("Recalibration method %s" % prep_params["recal"])
if requires_gatkfull:
runner = broad.runner_from_config(data["config"])
return runner.cl_gatk(args, tmp_dir)
else:
jvm_opts = broad.get_gatk_framework_opts(data["config"])
return broad.gatk_cmd("gatk-framework", jvm_opts, prep_params)
def _filter_paired(tumor, normal, out_file, reference, data):
"""filter paired vcf file with GATK
:param tumor: (str) sample name for tumor
:param normal: (str) sample name for normal
:param out_file: (str) final vcf file
:param reference: (str) genome in fasta format
:param data: (dict) information from yaml file(items[0])
:returns: (str) name of final vcf file
"""
in_file = utils.splitext_plus(out_file)[0] + "-tmp.vcf"
shutil.move(out_file, in_file)
config = data["config"]
with file_transaction(data, out_file) as tx_out_file:
params = ["-T", "SomaticPindelFilter", "-V", in_file, "-o",
tx_out_file, "-TID", tumor, "-NID", normal, "-R", reference]
jvm_opts = broad.get_gatk_opts(config)
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter pindel variants")
return out_file
def concat_variant_files(orig_files, out_file, regions, ref_file, config):
"""Concatenate multiple variant files from regions into a single output file.
Lightweight approach to merging VCF files split by regions with the same
sample information, so no complex merging needed. Handles both plain text
and bgzipped/tabix indexed outputs.
Falls back to bcftools concat if fails due to GATK stringency issues.
"""
if not utils.file_exists(out_file):
sorted_files = _sort_by_region(orig_files, regions, ref_file, config)
exist_files = [x for x in sorted_files if os.path.exists(x) and vcf_has_variants(x)]
if len(exist_files) == 0: # no non-empty inputs, merge the empty ones
exist_files = [x for x in sorted_files if os.path.exists(x)]
ready_files = run_multicore(p_bgzip_and_index, [[x, config] for x in exist_files], config)
input_file_list = "%s-files.list" % utils.splitext_plus(out_file)[0]
with open(input_file_list, "w") as out_handle:
for fname in ready_files:
out_handle.write(fname + "\n")
failed = False
with file_transaction(config, out_file) as tx_out_file:
params = ["org.broadinstitute.gatk.tools.CatVariants",
"-R", ref_file,
"-V", input_file_list,
"-out", tx_out_file,
"-assumeSorted"]
jvm_opts = broad.get_gatk_framework_opts(config, os.path.dirname(tx_out_file), include_gatk=False)
try:
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Concat variant files", log_error=False)
except subprocess.CalledProcessError as msg:
if ("We require all VCFs to have complete VCF headers" in str(msg) or
"Features added out of order" in str(msg) or
"The reference allele cannot be missing" in str(msg)):
os.remove(tx_out_file)
failed = True
else:
raise
if failed:
return _run_concat_variant_files_bcftools(input_file_list, out_file, config)
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
return out_file
def _filter_bad_reads(in_bam, ref_file, data):
"""Use GATK filter to remove problem reads which choke GATK and Picard.
"""
bam.index(in_bam, data["config"])
out_file = "%s-gatkfilter.bam" % os.path.splitext(in_bam)[0]
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
with file_transaction(data, out_file) as tx_out_file:
params = [
("FixMisencodedBaseQualityReads" if dd.get_quality_format(
data, "").lower() == "illumina" else "PrintReads"),
"-R", ref_file, "-I", in_bam, "-O", tx_out_file, "-RF",
"MatchingBasesAndQualsReadFilter", "-RF",
"SeqIsStoredReadFilter", "-RF", "CigarContainsNoNOperator"
]
jvm_opts = broad.get_gatk_opts(data["config"], tmp_dir)
do.run(broad.gatk_cmd("gatk", jvm_opts, params),
"Filter problem reads")
bam.index(out_file, data["config"])
return out_file
def genotype_filter(vcf_file, expression, data, name, filterext=""):
"""Perform genotype based filtering using GATK with the provided expression.
Adds FT tags to genotypes, rather than the general FILTER flag.
"""
base, ext = utils.splitext_plus(vcf_file)
out_file = "{base}-filter{filterext}{ext}".format(**locals())
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
params = ["-T", "VariantFiltration",
"-R", tz.get_in(["reference", "fasta", "base"], data),
"--variant", vcf_file,
"--out", tx_out_file,
"--genotypeFilterName", name,
"--genotypeFilterExpression", "'%s'" % expression]
jvm_opts = broad.get_gatk_framework_opts(data["config"], os.path.dirname(tx_out_file))
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter with expression: %s" % expression)
if out_file.endswith(".vcf.gz"):
out_file = vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
def _filter_bad_reads(in_bam, ref_file, data):
"""Use GATK filter to remove problem reads which choke GATK and Picard.
"""
bam.index(in_bam, data["config"])
out_file = "%s-gatkfilter.bam" % os.path.splitext(in_bam)[0]
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
with file_transaction(data, out_file) as tx_out_file:
params = ["-T", "PrintReads",
"-R", ref_file,
"-I", in_bam,
"--out", tx_out_file,
"--filter_mismatching_base_and_quals",
"--filter_bases_not_stored",
"--filter_reads_with_N_cigar"]
if dd.get_quality_format(data, "").lower() == "illumina":
params.append("--fix_misencoded_quality_scores")
jvm_opts = broad.get_gatk_framework_opts(data["config"], tmp_dir)
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter problem reads")
bam.index(out_file, data["config"])
return out_file
def _filter_bad_reads(in_bam, ref_file, data):
"""Use GATK filter to remove problem reads which choke GATK and Picard.
"""
bam.index(in_bam, data["config"])
out_file = "%s-gatkfilter.bam" % os.path.splitext(in_bam)[0]
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
with file_transaction(data, out_file) as tx_out_file:
params = ["-T", "PrintReads",
"-R", ref_file,
"-I", in_bam,
"--out", tx_out_file,
"--filter_mismatching_base_and_quals",
"--filter_bases_not_stored",
"--filter_reads_with_N_cigar"]
if dd.get_quality_format(data, "").lower() == "illumina":
params.append("--fix_misencoded_quality_scores")
jvm_opts = broad.get_gatk_framework_opts(data["config"], tmp_dir)
do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter problem reads")
bam.index(out_file, data["config"])
return out_file
def _gatk_extract_reads_cl(data, region, prep_params, tmp_dir):
"""Use GATK to extract reads from full BAM file, recalibrating if configured.
"""
requires_gatkfull = False
args = [
"-T", "PrintReads", "-L",
region_to_gatk(region), "-R", data["sam_ref"], "-I", data["work_bam"]
]
if prep_params["recal"] == "gatk":
if "prep_recal" in data and _recal_has_reads(data["prep_recal"]):
requires_gatkfull = True
args += ["-BQSR", data["prep_recal"]]
elif prep_params["recal"]:
raise NotImplementedError("Recalibration method %s" %
prep_params["recal"])
if requires_gatkfull:
runner = broad.runner_from_config(data["config"])
return runner.cl_gatk(args, tmp_dir)
else:
jvm_opts = broad.get_gatk_framework_opts(data["config"], tmp_dir)
return broad.gatk_cmd("gatk-framework", jvm_opts, args)
def _filter_bad_reads(in_bam, ref_file, data):
"""Use GATK filter to remove problem reads which choke GATK and Picard.
"""
bam.index(in_bam, data["config"])
out_file = "%s-gatkfilter.bam" % os.path.splitext(in_bam)[0]
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
with file_transaction(data, out_file) as tx_out_file:
params = [("FixMisencodedBaseQualityReads"
if dd.get_quality_format(data, "").lower() == "illumina"
else "PrintReads"),
"-R", ref_file,
"-I", in_bam,
"-O", tx_out_file,
"-RF", "MatchingBasesAndQualsReadFilter",
"-RF", "SeqIsStoredReadFilter",
"-RF", "CigarContainsNoNOperator"]
jvm_opts = broad.get_gatk_opts(data["config"], tmp_dir)
do.run(broad.gatk_cmd("gatk", jvm_opts, params), "Filter problem reads")
bam.index(out_file, data["config"])
return out_file