Hello everybody.

I have two main set of file to analyze, the end goal is SNP discovery and haplotype for posterior imputation.

One dataset is haploid the other is diploid. I will investigate each separatelly

For each dataset I have shallow sequenced DNA 26 individual trees.

My question is; there is any practical implication on doing the Variant calling for each individual then merge into a big vcf rather then merge all alignemnts in one big .bam (RG for each individual) and then do the variant call.

As far as I can see the differences in the individual call will be relativized by mergevcf tool, no?

Thanks in advance.

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