Question: merging vcf by vcftools
0
gravatar for mkamranazim
2.8 years 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 • 1.6k views
ADD COMMENTlink modified 4 months ago by l660811290 • written 2.8 years ago by mkamranazim0
2

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 2.8 years ago by Bastien Hervé4.9k

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 2.8 years ago by Kevin Blighe71k
1

I'm using picard MergeVcfs option and never had an issue with that... Maybe you should try it!

ADD REPLYlink written 4 months ago by brunobsouzaa510

i have the same problem,is there any answer later?

ADD REPLYlink written 4 months ago by l660811290
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