def format_pindel_vcf(input_vcf: str, output_vcf: str) -> None:
"""
Formats Pindel VCFs to work better with GDC downstream workflows.
:param input_vcf: The input VCF file to filter.
:param output_vcf: The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.
"""
logger = Logger.get_logger("format_pindel_vcf")
logger.info("Formats Pindel VCFs.")
# setup
total = 0
reader = pysam.VariantFile(input_vcf)
header = get_header(reader.header)
mode = get_pysam_outmode(output_vcf)
writer = pysam.VariantFile(output_vcf, mode=mode, header=header)
# Process
try:
for record in reader.fetch():
total += 1
tgt = record.samples["TUMOR"]["GT"]
flag = tgt == (0, 0)
if flag:
record.samples["TUMOR"]["GT"] = (0, 1)
# Info
new_info = get_info(record, flag)
# New record
new_record = writer.new_record()
new_record.contig = record.contig
new_record.alleles = record.alleles
new_record.start = record.start
new_record.stop = record.stop
new_record.id = record.id
new_record.qual = record.qual
for f in record.filter:
new_record.filter.add(f)
for i in new_info:
new_record.info[i[0]] = i[1]
for i, sample in enumerate(record.samples):
for k, v in record.samples[sample].items():
new_record.samples[i][k] = v
writer.write(new_record)
finally:
reader.close()
writer.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = pysam.tabix_index(output_vcf, preset="vcf", force=True)
logger.info("Processed {} records.".format(total))
def filter_nonstandard_variants(input_vcf: str, output_vcf: str) -> None:
"""
Remove non-ACTG loci from a VCF.
:param input_vcf: The input VCF file to filter.
:param output_vcf: The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.
"""
logger = Logger.get_logger("filter_nonstandard_variants")
logger.info("Drops non-ACTG loci from a VCF.")
# setup
total = 0
removed = 0
written = 0
# Full vcf reader
reader = pysam.VariantFile(input_vcf)
# Writer
mode = get_pysam_outmode(output_vcf)
writer = pysam.VariantFile(output_vcf, mode=mode, header=reader.header)
# Process
try:
for record in reader.fetch():
total += 1
alleles = list(''.join(list(record.alleles)).upper())
check = set(alleles) - ALLOWED_BASES
if check:
logger.warning("Removing {0}:{1}:{2}".format(
record.chrom, record.pos, ",".join(alleles)))
removed += 1
else:
written += 1
writer.write(record)
finally:
reader.close()
writer.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = pysam.tabix_index(output_vcf, preset="vcf", force=True)
logger.info("Processed {} records - Removed {}; Wrote {} ".format(
total, removed, written))
def dtoxog_maf_to_vcf(input_maf: str, reference_fa: str,
output_vcf: str) -> None:
"""
Transforms dToxoG MAF to minimal VCF of only dtoxo failures.
:param input_maf: The annotated dtoxog MAF output file.
:param reference_fa: Reference fasta used to make seqdict header.
:param output_vcf: The output minimal VCF with only failed dtoxog records BGzip and tabix-index created if ends with '.gz'.
"""
logger = Logger.get_logger("dtoxog_maf_to_vcf")
logger.info("Transforms dToxoG MAF to minimal VCF of dtoxo failures")
# setup
total = 0
written = 0
tag = "oxog"
# header
header = generate_header(reference_fa, tag)
# Writer
mode = get_pysam_outmode(output_vcf)
writer = VariantFile(output_vcf, mode=mode, header=header)
# Process
try:
with open(input_maf, "rt") as fh:
for record in maf_generator(fh):
total += 1
if record["oxoGCut"] == "1":
new_vcf_record = build_new_record(record, writer, tag)
writer.write(new_vcf_record)
written += 1
finally:
writer.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = tabix_index(output_vcf, preset="vcf", force=True)
logger.info("Processed {} records - Wrote {}".format(total, written))
def position_filter_dkfz(input_vcf: str, output_vcf: str) -> None:
"""
Removes VCF records where the POS-2 is less than 0 which
will cause an Exception to be thrown in DKFZBiasFilter. We
assume that the input VCF only contains SNPs, but no assertions
are made to validate this.
:param input_vcf: The input VCF file to filter.
:param output_vcf: The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.
"""
logger = Logger.get_logger("position_filter_dkfz")
logger.info("Position Filter for DKFZ.")
# setup
total = 0
removed = 0
written = 0
reader = pysam.VariantFile(input_vcf)
mode = get_pysam_outmode(output_vcf)
writer = pysam.VariantFile(output_vcf, mode=mode, header=reader.header)
# Process
try:
for record in reader.fetch():
total += 1
if record.pos - 2 < 0:
removed += 1
continue
written += 1
writer.write(record)
finally:
reader.close()
writer.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = pysam.tabix_index(output_vcf, preset="vcf", force=True)
logger.info("Processed {} records - Removed {}; Wrote {} ".format(
total, removed, written))
def add_oxog_filters(input_vcf: str, input_dtoxog: str,
output_vcf: str) -> None:
"""
Adds 'oxog' filter tag to VCFs.
:param input_vcf: The full input VCF file to filter.
:param input_dtoxog: The dtoxog VCF from dtoxog-maf-to-vcf used to annotate the full input VCF.
:param output_vcf: The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.
"""
logger = Logger.get_logger("add_oxog_filters")
logger.info("Adds dtoxog filters to VCF.")
# setup
total = 0
tagged = 0
written = 0
# Full vcf reader
reader = pysam.VariantFile(input_vcf)
filter_tag = "oxog"
reader.header.filters.add(filter_tag, None, None, "Failed dToxoG")
# Writer
mode = get_pysam_outmode(output_vcf)
writer = pysam.VariantFile(output_vcf, mode=mode, header=reader.header)
# dtoxog reader
dtoxog_reader = pysam.VariantFile(input_dtoxog)
# Process
try:
for record in reader.fetch():
total += 1
region = "{0}:{1}-{2}".format(record.contig, record.pos,
record.pos)
try:
for row in dtoxog_reader.fetch(region=region):
if record.pos == row.pos and record.ref.upper(
) == row.ref.upper():
# Add filter if failed oxog
record.filter.add("oxog")
tagged += 1
break
except ValueError:
pass
# handle case where the INFO column is '.'
for i in record.info:
if i == ".":
del record.info[i]
written += 1
writer.write(record)
finally:
reader.close()
writer.close()
dtoxog_reader.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = pysam.tabix_index(output_vcf, preset="vcf", force=True)
logger.info("Processed {} records - Tagged {}; Wrote {} ".format(
total, tagged, written))
def format_gdc_vcf(
input_vcf: str,
output_vcf: str,
patient_barcode: str,
case_id: str,
tumor_barcode: str,
tumor_aliquot_uuid: str,
tumor_bam_uuid: str,
normal_barcode: str,
normal_aliquot_uuid: str,
normal_bam_uuid: str,
*,
reference_name: str = "GRCh38.d1.vd1.fa",
) -> None:
"""
Adds VCF header metadata specific to the GDC.
:param input_vcf: The input VCF file to format.
:param output_vcf: The output formatted VCF file to create. BGzip and tabix-index created if ends with '.gz'.
:param patient_barcode: The case submitter id.
:param case_id: The case uuid.
:param tumor_barcode: The tumor aliquot submitter id.
:param tumor_aliquot_uuid: The tumor aliquot uuid.
:param tumor_bam_uuid: The tumor bam uuid.
:param normal_barcode: The normal aliquot submitter id.
:param normal_aliquot_uuid: The normal aliquot uuid.
:param normal_bam_uuid: The normal bam uuid.
:param reference_name: Reference name to use in header.
"""
logger = Logger.get_logger("format_gdc_vcf")
logger.info("Format GDC tumor/normal paired VCFs.")
# setup
reader = pysam.VariantFile(input_vcf)
mode = get_pysam_outmode(output_vcf)
# Load new header
new_header = build_header(
reader,
patient_barcode,
case_id,
tumor_barcode,
tumor_aliquot_uuid,
tumor_bam_uuid,
normal_barcode,
normal_aliquot_uuid,
normal_bam_uuid,
reference_name,
)
writer = pysam.VariantFile(output_vcf, mode=mode, header=new_header)
# Process
try:
for record in reader.fetch():
writer.write(record)
finally:
reader.close()
writer.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = pysam.tabix_index(output_vcf, preset="vcf", force=True)
def test_get_pysam_outmode(self):
mode = get_pysam_outmode("fake.vcf")
self.assertEqual(mode, "w")
mode = get_pysam_outmode("fake.vcf.gz")
self.assertEqual(mode, "wz")
def filter_somatic_score(
input_vcf: str,
output_vcf: str,
*,
tumor_sample_name: str = "TUMOR",
drop_somatic_score: int = 25,
min_somatic_score: int = 40,
) -> None:
"""
Filters SomaticSniper VCF files based on the Somatic Score.
:param input_vcf: The input VCF file to filter.
:param output_vcf: The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.
:param tumor_sample_name: The name of the tumor sample in the VCF.
:param drop_somatic_score: If the somatic score is < this, remove it.
:param min_somatic_score: If the somatic score is > drop_somatic_score and < this value, add ssc filter tag.
"""
logger = Logger.get_logger("filter_somatic_score")
logger.info("Filters SomaticSniper VCF files based on Somatic Score.")
# setup
total = 0
removed = 0
tagged = 0
written = 0
reader = pysam.VariantFile(input_vcf)
filter_tag = "ssc{0}".format(min_somatic_score)
logger.info("Filter tag: {}".format(filter_tag))
reader.header.filters.add(filter_tag, None, None,
"Somatic Score < {0}".format(min_somatic_score))
mode = get_pysam_outmode(output_vcf)
writer = pysam.VariantFile(output_vcf, mode=mode, header=reader.header)
# Process
try:
for record in reader.fetch():
total += 1
ssc = record.samples[tumor_sample_name]["SSC"]
if ssc < drop_somatic_score:
removed += 1
continue
elif ssc < min_somatic_score:
tagged += 1
record.filter.add(filter_tag)
written += 1
writer.write(record)
finally:
reader.close()
writer.close()
if mode == "wz":
logger.info("Creating tabix index...")
tbx = pysam.tabix_index(output_vcf, preset="vcf", force=True)
logger.info(
"Processed {} records - Removed {}; Tagged {}; Wrote {} ".format(
total, removed, tagged, written))