varscan copy number error
I am running varscan2 and it shows me this error and gives a blank output.copynumber only with the headers and this error on the terminal:
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from Normal-SL100.mpileup
Reading mpileup input...
Parsing Exception on line:
chrM 15655 T 0 * * 0
8
I created mpileup file for normal and tumor with the following command:
> samtools mpileup -f ucsc.hg19.fasta -d 8000 -A -E Normal.bam Tumor.bam | awk '{if($4 != 0) print $0}' > Normal-Tumor.mpileup
Thank you
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I suspect that your
| awk '{if($4 != 0) print $0}'is removing the header from the raw mpileup file. Try using| awk '{if($4 != 0 || substr($1, 0, 1)=="#") print $0}'instead.