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Old 02-20-2014, 06:21 AM   #1
RBCT
Junior Member
 
Location: MN

Join Date: Feb 2014
Posts: 1
Default VarScan- invalid format for pileup

Hello,

I've used the following command to filter my BAM file, run samtools pileup and varscan:

samtools view -b -q 10 myBam.bam | samtools mpileup -f myRef.fasta -
| java –jar VarScan.v2.3.6.jar pileup2snp --min-coverage 6 --min-avg-qual 4 --min-var-freq 0.01 --p-value 0.05

The program ran for a while and then I got this error:

Error: Invalid format for pileup at line 820808910
chr18 74082743

It seems like a lot of people have had this issue before but I don't know how to fix it. Any help will be greatly appreciated. Thanks!!
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Old 02-27-2014, 09:37 AM   #2
nnutter
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Location: Illinois, United States

Join Date: Mar 2013
Posts: 5
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I can't really offer any help but it might be useful to split that pipe of three commands into separate steps so you can figure out which tool is throwing the error.
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