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Old 03-02-2015, 04:14 AM   #1
Location: US

Join Date: Apr 2010
Posts: 63
Default vcf file - filter based on DP4 (not total) and removal alternative alleles

Hi all,

I'm using samtools/mpileup to find variants in my resequencing data of multiple samples together. I and got one vcf file with SNPs and Indels.
I am applying many different filtrations but I would like to filter based on strand bias, for example

Chr1_66769 G A 135 PASS DP=259;VDB=9.53273e-06;SGB=-37.5721;RPB=0.988496;MQB=2.5526e-0
6;MQSB=0.0499642;BQB=0.235831;MQ0F=0;ICB=0.0671329;HOB=0.0246914;AC=6;AN=54;DP4=87,156,0,10 ...

I would like to remove variants with 0 reads in the forward or reverse strand for the alternative allele. In other words variant supported by both forward and reverse strands.

I did not find any command to do it, only manual. Any suggestion?

Other question is how to remove from vcf file the alternative alleles, I do not want this info in my filtered file.

Chr11_6676982 C G,A .....

I would like to have
Chr11_6676982 C G .....

Thanks very much

Last edited by clarissaboschi; 03-17-2015 at 08:41 AM. Reason: grammar
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