Re: [Vcftools-help] vcftools filter

[Anthony M. <ant...@ei...>]

Jeremy,

In vcftools the minor allele is just the allele with the lowest allele count. In this case, the reference allele is counted as the minor allele and since there aren't any calls for the reference allele, this site is filtered out.

You should be using the following filters:
--non-ref-af-any <float> 
--max-non-ref-af-any <float> 

Let me know if you have any further questions.

--
Anthony Marcketta
Bioinformatics Analyst
Department of Genetics
Albert Einstein College of Medicine
Price Center 353D
Bronx, New York 10461
________________________________________
From: Adrian Pelin [ape...@gm...]
Sent: Friday, April 10, 2015 7:46 PM
To: Jeremy Chien
Cc: vcf...@li...
Subject: Re: [Vcftools-help] vcftools filter

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...<mailto: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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