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Old 01-20-2013, 10:40 AM   #1
Junior Member
Location: Los Angeles

Join Date: Jan 2013
Posts: 1
Default VarScan early halt


I'm new to VarScan. I was trying to call copynumber from my exome sequencing data.

My script is
samtools mpileup -q 1 -f ~/hg19.fa normal.rmdup.bam tumor.rmdup.bam | java -Xmx4g -jar ~/VarScan.v2.3.3.jar copynumber > output --mpileup 1

It seems to run the first bit of the program and start to generate 2 files
1. copynumber
But it halted when it went to
chrM 16066 16165 100 53.7 89.7 0.740 1.0

The other file 30.copynumber only has the column name
chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content

Running message is as following:
[mpileup] 1 samples in 2 input files
<mpileup> Set max per-file depth to 8000
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from STDIN
Reading mpileup input...
Parsing Exception on line:
chrM 16184 C 0 0

It seems that something happened at the site chrM 16184... But I used my bam files to call SNPs/coverage from gatk and they worked out fine... I didn't know what's wrong...

Many thanks,
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