Question: bcftools merge single-sample vcf files
0
gravatar for j.lunger18
6 months ago by
j.lunger1810
j.lunger1810 wrote:

Hi. I'm trying to merge .vcf files from TCGA. Each of these files is from a single sample, which is indicated by the file name. However, the vcf file header contains the following for each sample:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR

When I try to merge, I get the error:

Error: Duplicate sample names (NORMAL), use --force-samples to proceed anyway.

I could replace NORMAL with the file name so that I can associate each annotation with the correct ID, but I'm wondering if I have to do this. Will --force-samples remove information?

snp bcftools vcf • 183 views
ADD COMMENTlink modified 6 months ago by WouterDeCoster44k • written 6 months ago by j.lunger1810
1
gravatar for WouterDeCoster
6 months ago by
Belgium
WouterDeCoster44k wrote:

I would suggest doing bcftools reheader to change all sample names per file to ID-N and ID-T before merging. If not you won't be able to query which Tumor and Normal belong to the same individual.

ADD COMMENTlink written 6 months ago by WouterDeCoster44k

Thanks, I'll look into it.

ADD REPLYlink written 6 months ago by j.lunger1810
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