Varscan and mpileup

[aunderwo]

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

However
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

[dkoboldt]

Hello,

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

[aunderwo]

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.