question of varscan filter
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15 months ago
duolin1 ▴ 10

I am trying to find de novo mutation snp from trio; I get a trio vcf, then I use varscan filter command to get more real de novo mutation snp, this is my command varscan filter trio.mpileup.output.snp.vcf --p-value 0.01 --indel-file trio.mpileup.output.indel.vcf > filtered.output.snp.vcf, output is Min coverage: 10; Min reads2: 2; Min strands2: 1 ;Min var freq: 0.2 ;Min avg qual: 15; P-value thresh: 0.01, finaly, I get a wired snp "chr1 19391 . G A . PASS ADP=21;STATUS=1 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:25:13:13:6:7:53.85%:2.6087E-3:37:35:0:6:0:7 0/1:15:28:28:23:5:17.86%:2.5729E-2:37:34:0:23:0:5 0/0:31:22:22:21:1:4.55%:5E-1:37:37:0:21:0:1", the order is father-mother-child, I know 0/1-0/1-0/0 means untransmitted; but I filter with argument p-value 0.01, why does this site pass filter? by the way, if I set p-value 0.001, then this site will disapper.

snp varscan • 501 views

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