Question: Is this the good way to parse var.vcf files ?
0
gravatar for jsgounot
3.6 years ago by
jsgounot130
European Union
jsgounot130 wrote:

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 • 913 views
ADD COMMENTlink modified 3.6 years ago by vassialk190 • written 3.6 years ago by jsgounot130

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

ADD REPLYlink written 3.6 years ago by RamRS21k
0
gravatar for vassialk
3.6 years ago by
vassialk190
Belarus
vassialk190 wrote:

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

ADD COMMENTlink written 3.6 years ago by vassialk190

Where is the sourceforge link?

Thanks

ADD REPLYlink written 3.2 years ago by onemoreuser10

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

ADD REPLYlink written 3.2 years ago by RamRS21k

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 REPLYlink written 3.2 years ago by onemoreuser10

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

ADD REPLYlink written 3.2 years ago by RamRS21k
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