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Old 01-15-2012, 04:17 PM   #1
phatjoe
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Location: Asia

Join Date: Aug 2011
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Default VCF file, missing AA, AC and AN tags

I am current using samtools version 0.1.16 (r963:234) where it generates a 4.1 version vcf file. This is a sample of my vcf file where at the Info column I dont see any AC,AN,AF and AA tags as shown in the sample of the 1000 genome vcf format.

Quote:
ctg111 513203 . C T 39 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,1,4,2;MQ=37;FQ=42;PV4=1,1.1e-07,1,1 GT:PL:GQ 0/1:69,0,138:72

I am currently looking for a way to check the ALT allele counts and would like to know how do I get the informations of these (AA,AC,AF and AN ) tags?

Many thanks

Cheers!
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