Is this the good way to parse var.vcf files ?
1
0
Entering edit mode
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
ADD COMMENT
0
Entering edit mode

Ummm, what are var.vcf files? Are they a special type of VCF files?

ADD REPLY
0
Entering edit mode
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.

ADD COMMENT
0
Entering edit mode

Where is the sourceforge link?

Thanks

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1789 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6