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Old 09-14-2011, 11:39 PM   #1
Delphine Song
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Location: China

Join Date: Aug 2011
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Question Does VarScan have a preferred choromosome order?

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?
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Old 09-16-2011, 01:48 AM   #2
sdvie
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Location: Spain

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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
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Old 09-28-2011, 07:46 PM   #3
Delphine Song
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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.
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