varscan copy number error

Question

[mittu1602]

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

[Matteo Schiavinato]

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.