Hi,
I am trying to filter the variants using vcfutils.pl script.
Usage: vcfutils.pl varFilter [options] <in.vcf>
Options: -Q INT minimum RMS mapping quality for SNPs [10]
-d INT minimum read depth [2]
-D INT maximum read depth [10000000]
-a INT minimum number of alternate bases [2]
-w INT SNP within INT bp around a gap to be filtered [3]
-W INT window size for filtering adjacent gaps [10]
-1 FLOAT min P-value for strand bias (given PV4) [0.0001]
-2 FLOAT min P-value for baseQ bias [1e-100]
-3 FLOAT min P-value for mapQ bias [0]
-4 FLOAT min P-value for end distance bias [0.0001]
-e FLOAT min P-value for HWE (plus F<0) [0.0001]
-p print filtered variants
Could someone suggest an ideal strand bias threshold to use? Searched
the forum and there are many unanswered questions regarding this. Would
be great if someone can answer.
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