Hello Samtool community,
I have two vcf files each with 1000 individuals. I would like to know the
best way to analyze the data together. Is it OK to merge these two vcf
files or should I run the samtool mpileup on 2000 bam file to generate
single vcf file for 2000 individuals? I heard that, for getting best calls
for rare alleles, running mpileup on 2000 samples is recommended.
Thanks and regards
Sandip
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