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  • Error: Invalid format for pileup at line null in varscan2

    Hi,

    I am using Varscan2 with readcounts like follows

    Code:
    samtools mpileup -f /home/tsekara/Transcriptomes/trinity5_frameDPcorrected.fa /home/tsekara/David_Schmidt/Bowtie2_default/Sorted_bams/Sorted_Sample_60_EdU48h1mg.bam | java -jar ./bin/VarScan.v2.3.9.jar readcounts --output-vcf > sample.vcf
    but after sometime it gives me error saying that
    Code:
    Error: Invalid format for pileup at line null
    How could I solve this error. Kindly guide me.

  • #2
    mpileup format

    Hi,

    I had the same issue and it turns out that VarScan readcount crashes if the fourth column (number of reads covering the site) is 0.
    Try to filter for those manually, e.g.:


    HTML Code:
    samtools mpileup -f /home/tsekara/Transcriptomes/trinity5_frameDPcorrected.fa /home/tsekara/David_Schmidt/Bowtie2_default/Sorted_bams/Sorted_Sample_60_EdU48h1mg.bam |awk '($4>0)' | java -jar ./bin/VarScan.v2.3.9.jar readcounts --output-vcf > sample.vcf
    That worked for me.

    Rob
    Last edited by RobUK; 12-14-2015, 08:56 AM. Reason: copy and paste error in the awk command

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