How to filter out SNPs with Minor allele frequency less than 5% in VCF file

jdpr_100 · 09-30-2014, 07:40 AM

Hello,
I would like to filter out SNPs with allele frequencies in VCF file from multi-sample variant calling.
I tried VCFtools with the following commands, but it doesn't work.

Quote:

vcftools --vcf input.vcf --recode --recode-INFO-all --stdout --maf 0.05 --max-maf 1 --out outpur.vcf

Here is the vcf file format generated from samtools mpileup.

Quote:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 788 712 908 544 541 581 801 381 479 487 379 570
Chr01 11356 . C A 124 . DP=88;VDB=1.624097e-04;RPB=-2.346857e+00;AF1=0.1553;AC1=3;DP4=75,3,10,0;MQ=30;FQ=124;PV4=1,1,1,1
GT:PL

P:GQ 0/0:0,0,0:0:5 0/0:0,6,59:2:11 0/0:0,0,0:0:5 0/1:28,0,123:8:24 1/1:157,24,0:8:14 0/0:0,39,221:13:43 0/0:0,12,85:4
:17 0/0:0,36,164:12:40 0/0:0,39,147:13:43 0/0:0,9,71:3:14 0/0:0,48,163:16:52 0/0:0,27,126:9:31
Chr01 11384 . T C 15.9 . DP=123;VDB=5.617680e-03;RPB=1.820871e+00;AF1=0.04721;AC1=1;DP4=114,3,5,0;MQ=31;FQ=16.1;PV4=1,1,0.05,1 GT:PL

P:GQ 0/0:0,12,79:4:22 0/0:0,6,60:2:16 0/0:0,0,0:0:10 0/0:0,30,163:10:40 0/0:0,27,159:9:37 0/0:0,60,244:20:70 0/0:0,12,85:4:22 0/0:0,48,163:16:58 0/1:56,0,116:15:46 0/0:0,18,122:6:28 0/0:0,69,185:23:79 0/0:0,39,135:13:49

I wonder if anyone could help me
Thanks

swbarnes2 · 10-01-2014, 03:14 PM

The DP4 part spells out how many reads aligned to reference and alternate allele. So you can parse based on that. You could do that with some finagling in Excel, if you had to.

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10-01-2014, 03:14 PM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	The DP4 part spells out how many reads aligned to reference and alternate allele. So you can parse based on that. You could do that with some finagling in Excel, if you had to.