Question: vcftools keep only indels not working
0
gravatar for t86dan
2.7 years ago by
t86dan30
t86dan30 wrote:

Hi, I am trying to filter a vcf file so that I only get indels from it. I am using vcftools with the following command:

vcftools --vcf NIST_RTG_PlatGen_merged_highconfidence_v0.2_Allannotate.vcf --max-alleles 2 --min-alleles 2 --keep-only-indels --recode --recode-INFO-all --out indels

I get the following error:

Error: Flag Type must have 0 entries: ID=isPolymorphic,Number=1,Type=Flag,Description="Sites that are polymorphic in the CEPH1493 pedigree

First time I see this kind of error, I have been filtering vcf files without problems until now. Any idea why vcftools it not filtering this particular vcf?

Thanks!

software error • 1.8k views
ADD COMMENTlink modified 2.7 years ago by Pierre Lindenbaum129k • written 2.7 years ago by t86dan30
0
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

The error is raised here: https://github.com/vcftools/vcftools/blob/master/src/cpp/header.cpp#L141

in your VCF header you should have:

##INFO=<ID=isPolymorphic,Number=0,Type=Flag,Description="Sites...

instead of

##INFO=<ID=isPolymorphic,Number=1,Type=Flag,Description="Sites...

use sed to fix this.

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum129k

Okay, thanks!

How can I change that though?

ADD REPLYlink written 2.7 years ago by t86dan30

as mentioned by @pierre lindenbaum by

sed

ADD REPLYlink written 2.7 years ago by mittu1602180
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