merging vcf by vcftools
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
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mkamranazim •
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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.
In addition to the above, you should use BCFtools (
mergeorconcat, 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.i have the same problem,is there any answer later?
I'm using
picard MergeVcfsoption and never had an issue with that... Maybe you should try it!