Is this the good way to parse var.vcf files ?
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7.1 years ago
jsgounot ▴ 170

Hi everyone,

I have to parse var.vcf files for my work and I'm wondering if I'm doing this correctly. For example with this line :

Chr1    204346    .    G    A,C    138    .    DP=360;VDB=0.0143;AF1=1;AC1=2;DP4=1,1,208,126;MQ=35;FQ=-282;PV4=1,0.01,0.48,1    PL    171,255,0,172,35,25

First I check for all bases possibilites : GG, GA, AA, GC, CA, CC

After that I look at the PL field and choose the bases with the index of the lowest value in this field.

So in my case it will be AA.

Is this correct ?

snp • 1.7k views
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Ummm, what are var.vcf files? Are they a special type of VCF files?

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7.1 years ago
vassialk ▴ 200

Perhaps, you can use VCF tools and software libraries of R, Python, Ruby, Java, C++. See the sourceforge for details.

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Thanks

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vcftools (with its documentation) is now on GitHub. Avoid SourceForge because they bundle in junkware with their software installers.

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I was referring to the libraries. I don't know many libraries in Java to process vcf files. Do you know any? Until now I only used htsjdk.

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Sorry, I'm not a Java person. Maybe Pierre Lindenbaum or Brian Bushnell can help.