Error: Invalid format for pileup at line null in varscan2

[dena.dinesh]

Hi,

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.

[RobUK]

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.:

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