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Old 11-04-2011, 09:50 AM   #1
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Location: London

Join Date: Jan 2009
Posts: 6
Default Varscan and mpileup

Hi all

does anybody gave any experience in using mpileup and then using varscans new mpileup2snp function to call SNPs?

I have generated 2 bam files and then used samtols mpileup to produce a pileup file

samtools mpileup -f ref.fas sample1.bam sample2.bam > out.pileup

java -jar VarScan.v2.2.8.jar mpileup2snp --min-coverage 10 --min-var-freq 0.9 --min-reads2 9 --strand-filter < out.pileup

throws an exception

Input Parameter Threw Exception: For input string: "out.pileup"

running the equivalent pileup command works but with no SNPs

java -jar VarScan.v2.2.8.jar pileup2snp --min-coverage 10 --min-var-freq 0.9 --min-reads2 9 --strand-filter < out.pileup

This suggests I am not getting the correct mpileup file that Varscan expects.

Please can someone advise on the correct procedure.

Thanks Anthony
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Old 11-04-2011, 11:38 AM   #2
Location: St. Louis

Join Date: Mar 2009
Posts: 62


I believe that you are using the command incorrectly. The input file should come after the VarScan subcommand, e.g.:

java -jar VarScan.v2.2.8.jar mpileup2snp out.pileup --min-coverage 10 --min-var-freq 0.9 --min-reads2 9 --strand-filter
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Old 11-05-2011, 03:43 AM   #3
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Location: London

Join Date: Jan 2009
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It turns out that you can specify the input either as mpileup2snp out.pileup options OR mpileup2snp options < out.pileup.

The problem was --strand-filter needs an option (1 for on, 0 for off)

However now I need to find out how to interpret the mpileup2snp output. Can't see anything on the varscan site.
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