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Old 08-14-2015, 05:54 AM   #1
Location: Europe

Join Date: Feb 2013
Posts: 58
Default Error: Invalid format for pileup at line null in varscan2


I am using Varscan2 with readcounts like follows

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
Error: Invalid format for pileup at line null
How could I solve this error. Kindly guide me.
dena.dinesh is offline   Reply With Quote
Old 12-14-2015, 07:27 AM   #2
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Location: UK

Join Date: Dec 2015
Posts: 1
Default mpileup format


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.


Last edited by RobUK; 12-14-2015 at 07:56 AM. Reason: copy and paste error in the awk command
RobUK is offline   Reply With Quote

pileup, rnaseq, variant analysis, varscan2

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