Question: merging vcf by vcftools
gravatar for mkamranazim
21 months ago by
mkamranazim0 wrote:

Dear All I have tried to merge two vcf files by using vcf-sort, gzip, tablix followed by vcf-merge. The resultant merged file contains variants on chromosome 1 only. Any comment/help would be appreciated.

Regards Kamran Azim

sequencing snp next-gen genome • 1.1k views
ADD COMMENTlink written 21 months ago by mkamranazim0

With all respect, how can we help with these informations ?

We need to have a look at the command lines you used, the VCFs you are working on (or at least a representative parts of these VCFs) and the result you get.

ADD REPLYlink written 21 months ago by Bastien Hervé4.5k

In addition to the above, you should use BCFtools (merge or concat, depending on what exactly you're doing) and not VCFtools. There's even a written line somewhere by one of the authors of VCFtools where he encourages people to switch to BCFtools.

ADD REPLYlink written 21 months ago by Kevin Blighe54k
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