merging vcf by vcftools
0
0
Entering edit mode
6.6 years ago

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
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
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
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1634 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6