Combining per sample vcf files into multisample vcf

[danangcrysnanto]

Hi

Thanks for the great tools. Is there any recommendation (or capability in xatlas) to merge single sample vcf produced by xatlas to the multi sample vcf. I have tried several possibility:

• Run the xatlas in vcf mode and then combined using a simple bcftools merge . But there is a no way to differentiate between no call ./. to the homozygous reference 0/0 and i found that bcftools infers all non-variants site to be missing
• Run the xatlas in gvcf mode and then combined using gvcftools merge_variants. However, the gvcftools does not recommended to do this I am usually do imputation after variant calling. Thus the differentiation between non-ref and missing is important.

Thanks in advance for the help.

[jfarek]

Hi,

xAtlas itself performs only single-sample variant calling. For creating multi-sample VCFs and pVCFs, our group has been using a version of GLNexus for the gVCF merging steps. GLNexus is more on the heavy side compared to bcftools and gvcftools, but we have found it a very useful tool for our analyses. We haven't attempted to merge xAtlas VCFs or gVCFs with either bcftools or gvcftools.

[danangcrysnanto]

Hi Appreciate for your feedback. I will try the GLnexus.