def spv_freq_filter(line, tumor_index):
"""Filter VarScan calls based on the SPV value and frequency.
Removes calls with SPV < 0.05 and a tumor FREQ > 0.35.
False positives dominate these higher frequency, low SPV calls. They appear
to be primarily non-somatic/germline variants not removed by other filters.
"""
if line.startswith("#CHROM"):
headers = [('##FILTER=<ID=SpvFreq,Description="High frequency (tumor FREQ > 0.35) '
'and low p-value for somatic (SPV < 0.05)">')]
return "\n".join(headers) + "\n" + line
elif line.startswith("#"):
return line
else:
parts = line.split("\t")
sample_ft = {a: v for (a, v) in zip(parts[8].split(":"), parts[9 + tumor_index].split(":"))}
freq = utils.safe_to_float(sample_ft.get("FREQ"))
spvs = [x for x in parts[7].split(";") if x.startswith("SPV=")]
spv = utils.safe_to_float(spvs[0].split("=")[-1] if spvs else None)
fname = None
if spv is not None and freq is not None:
if spv < 0.05 and freq > 0.35:
fname = "SpvFreq"
if fname:
if parts[6] in set([".", "PASS"]):
parts[6] = fname
else:
parts[6] += ";%s" % fname
line = "\t".join(parts)
return line
def spv_freq_filter(line, tumor_index):
"""Filter VarScan calls based on the SPV value and frequency.
Removes calls with SPV < 0.05 and a tumor FREQ > 0.35.
False positives dominate these higher frequency, low SPV calls. They appear
to be primarily non-somatic/germline variants not removed by other filters.
"""
if line.startswith("#CHROM"):
headers = [(
'##FILTER=<ID=SpvFreq,Description="High frequency (tumor FREQ > 0.35) '
'and low p-value for somatic (SPV < 0.05)">')]
return "\n".join(headers) + "\n" + line
elif line.startswith("#"):
return line
else:
parts = line.split("\t")
sample_ft = {
a: v
for (a,
v) in zip(parts[8].split(":"), parts[9 +
tumor_index].split(":"))
}
freq = utils.safe_to_float(sample_ft.get("FREQ"))
spvs = [x for x in parts[7].split(";") if x.startswith("SPV=")]
spv = utils.safe_to_float(spvs[0].split("=")[-1] if spvs else None)
fname = None
if spv is not None and freq is not None:
if spv < 0.05 and freq > 0.35:
fname = "SpvFreq"
if fname:
if parts[6] in set([".", "PASS"]):
parts[6] = fname
else:
parts[6] += ";%s" % fname
line = "\t".join(parts)
return line
def depth_freq_filter(line, tumor_index, aligner):
"""Command line to filter VarDict calls based on depth, frequency and quality.
Looks at regions with low depth for allele frequency (AF * DP < 6, the equivalent
of < 13bp for heterogygote calls, but generalized. Within these calls filters if a
calls has:
- Low mapping quality and multiple mismatches in a read (NM)
For bwa only: MQ < 55.0 and NM > 1.0 or MQ < 60.0 and NM > 2.0
- Low depth (DP < 10)
- Low QUAL (QUAL < 45)
Also filters in low allele frequency regions with poor quality, if all of these are
true:
- Allele frequency < 0.2
- Quality < 55
- P-value (SSF) > 0.06
"""
if line.startswith("#CHROM"):
headers = [('##FILTER=<ID=LowAlleleDepth,Description="Low depth per allele frequency '
'along with poor depth, quality, mapping quality and read mismatches.">'),
('##FILTER=<ID=LowFreqQuality,Description="Low frequency read with '
'poor quality and p-value (SSF).">')]
return "\n".join(headers) + "\n" + line
elif line.startswith("#"):
return line
else:
parts = line.split("\t")
sample_ft = {a: v for (a, v) in zip(parts[8].split(":"), parts[9 + tumor_index].split(":"))}
qual = utils.safe_to_float(parts[5])
dp = utils.safe_to_float(sample_ft.get("DP"))
af = utils.safe_to_float(sample_ft.get("AF"))
nm = utils.safe_to_float(sample_ft.get("NM"))
mq = utils.safe_to_float(sample_ft.get("MQ"))
ssfs = [x for x in parts[7].split(";") if x.startswith("SSF=")]
pval = utils.safe_to_float(ssfs[0].split("=")[-1] if ssfs else None)
fname = None
if not chromhacks.is_sex(parts[0]) and dp is not None and af is not None:
if dp * af < 6:
if aligner == "bwa" and nm is not None and mq is not None:
if (mq < 55.0 and nm > 1.0) or (mq < 60.0 and nm > 2.0):
fname = "LowAlleleDepth"
if dp < 10:
fname = "LowAlleleDepth"
if qual is not None and qual < 45:
fname = "LowAlleleDepth"
if af is not None and qual is not None and pval is not None:
if af < 0.2 and qual < 45 and pval > 0.06:
fname = "LowFreqQuality"
if fname:
if parts[6] in set([".", "PASS"]):
parts[6] = fname
else:
parts[6] += ";%s" % fname
line = "\t".join(parts)
return line
