merging vcf by vcftools

0

Entering edit mode

6.6 years ago

mkamranazim • 0

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

next-gen sequencing SNP genome • 2.6k views

ADD COMMENT • link updated 4.1 years ago by l66081129 • 0 • written 6.6 years ago by mkamranazim • 0

2

Entering edit mode

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 REPLY • link 6.6 years ago by Bastien Hervé 5.9k

0

Entering edit mode

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 REPLY • link 6.6 years ago by Kevin Blighe 88k

1

Entering edit mode

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