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Old 02-20-2014, 07:21 AM   #1
Junior Member
Location: MN

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


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!!
RBCT is offline   Reply With Quote
Old 02-27-2014, 10:37 AM   #2
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Location: Illinois, United States

Join Date: Mar 2013
Posts: 5

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.
nnutter is offline   Reply With Quote

error pileup, mpileup, varscan

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