Question: How to add info to the sample columns of a VCF?
0
gravatar for Niek De Klein
2.1 years ago by
Niek De Klein2.4k
Netherlands
Niek De Klein2.4k wrote:

Is there a tool that can add information to the sample columns of a VCF file, similar to bcftools --annotations but instead of changing the INFO column the FORMAT column + all the sample information? So if I have the line

20  14370   rs6054257 G   A    29   PASS   NS=3;DP=14;AF=0.5;DB;H2     GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.

I would like to add sample info :I with a number:

20  14370   rs6054257 G   A   29   PASS   NS=3;DP=14;AF=0.5;DB;H2      GT:GQ:DP:HQ:I 0|0:48:1:51,51:3 1|0:48:8:51,51:4 1/1:43:5:.,.:6

With a different number for each of the samples.

bcftools vcf • 1.1k views
ADD COMMENTlink written 2.1 years ago by Niek De Klein2.4k

what would be your input for the 'I', another VCF ?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Pierre Lindenbaum114k

I have a tab delimited file

 sample_name      snp CHR        SNP pos          value

but I can put it in a different format.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Niek De Klein2.4k

for ALL the positions ?

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum114k

Yes, saw my mistake and edited it

ADD REPLYlink written 2.1 years ago by Niek De Klein2.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 770 users visited in the last hour