Re: [Vcftools-help] vcftools filter

[Adrian P. <ape...@gm...>]

What do your tags mean? you are asking for --max-maf 1, which tags help
determining the MAF, besides AF=1.0. In other words, out of 170 reads which
cover the position (DP) how many are REF and how many are ALT?

On Fri, Apr 10, 2015 at 7:29 PM, Jeremy Chien <jc...@ku...> wrote:

> Hello,
>
> I have the following entry in the my.vcf file.
>
> chr17   7578205 .       C       A       5631.90 PASS
> AC=2;AF=1.00;AN=2;BaseQRankSum=0.683;CODING=1;DJ=29;DP=170;Dels=0.00;ED=1;FS=3.565;HRun=1;HaplotypeScore=3.9983;MQ=50.00;MQ0=0;MQRankSum=-0.921;OrgScore=0.51587;PctExtPos=0.18;QD=33.13;QScore=0.84249;ReadPosRankSum=-2.080;SB=-2320.78;SNPEFF_AMINO_ACID_CHANGE=S176I;SNPEFF_AMINO_ACID_LENGTH=354;SNPEFF_CODON_CHANGE=aGt/aTt;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=NM_001126118.ex.6;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_NAME=TP53;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=NM_001126118;SplitReadPosRankSum=1.318
>       GT:AD:DP:DP4:GQ:PL      1/1:7,162:170:4,3,64,98:99:5632,185,0
>
> When I run the command,
> vcftools_0.1.12b/bin/vcftools --vcf my.vcf --out my.vcf.cov20freq20
> --min-meanDP 20 --maf 0.2 --max-maf 1.0 --recode
>
> The variant was filter out. This is a variant I want to keep for
> downstream processing.  I thought I am filtering out only low coverage
> variants (<20 read-depth) and low frequency variants (<20%). This variant
> has DP > 20 and maf > .2.  It should not have been flltered out. Did I do
> something wrong?
>
> Thanks,
> Jeremy
>
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