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  • 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!!

  • #2
    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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