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Old 09-30-2014, 06:40 AM   #1
jdpr_100
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Location: Gaineville FL

Join Date: Jun 2014
Posts: 14
Default How to filter out SNPs with Minor allele frequency less than 5% in VCF file

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:PLP: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:PLP: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
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