these days ,i have been doing call snp with my multiple samples` RNA-seq data , and i read two workflow:A and B
so i got some questions below:
1.i want use workflow B to call snp for my every single sample data . so i will get several vcf files , can i just use MergeVCFs to combine them in the end ? is this kind of way is good to work?
2.i still have some confusion about MergeVCFs : as i see , this tools can get a union set from many many vcf files (maybe my expression is no so clear 
) .
e.g:i got a VCF from sampleA and a VCF from sampleB . their have different variations , but the MergeVCFs will deliver a VCF that contain all the variation from both of them.
thanks a lot.
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can this workflow work?
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