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
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
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