[Samtools-help] merging vcf files

[Sandip K. <vsk...@gm...>]

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