Does VarScan have a preferred choromosome order?

[Delphine Song]

Hi all,

I'm running VarScan somatic with 2 samples. But the outputs of snp and indel only contain information of chrM, chrX, and chrY. And the log file reports,"Resetting normal file because chrY_random > chrUn_random" .
So, I'm wondering where the problem is. Does VarScan have a preferred choromosome order?

[sdvie]

Hi,

what do you do before running varscan?
We usually sort the bam files (samtools sort), then generate the pileups (samtools mpileup) and then run varscan somatic, and this works fine.

cheers,
Sophia

[Delphine Song]

Thanks for the answer.

It turns out that I forgot to sort one of my bam files.

Now I've sorted it and it works well.