NOT RESETTING NORMAL error using Varscan2
Entering edit mode
9.5 years ago
Jordan ★ 1.3k


I'm running Varscan2 somatic caller for my analysis. I'm getting an error which I never received before.

Not resetting normal file because chrM < chrY
Not resetting normal file because chrM < chrY
Not resetting normal file because chrM < chrY
Not resetting normal file because chrM < chrY
Not resetting normal file because chrM < chrY
99899966 positions in tumor
96924664 positions shared in normal
5452161 had sufficient coverage for comparison
5444310 were called Reference
0 were mixed SNP-indel calls and filtered
6507 were called Germline
191 were called LOH
1102 were called Somatic
51 were called Unknown
0 were called Variant

The vcf files are being generated with variants in them. But I'm not sure why this warning/error is being reported. The BAM file is position sorted using samtools as well.

I ran MuTect on the sample and had no complaints.

Here is my code:

java -Xmx16g -jar /usr/local/packages/VarScan/2.3.6/VarScan.jar somatic Normal.pileup Tumor.pileup --output-snp sample.snp --output-indel sample.indel --output-vcf 1

Any help is appreciated. Thanks!

varscan2 variant-calling SNP somatic • 4.6k views
Entering edit mode
Entering edit mode

I did what was suggested. I have a new problem now. There are no variants being generated.

I used the following code:

samtools mpileup -q 10 -f hg19.fasta -B normal.bam tumor.bam > normal-tumor.pileup

java -XX:ParallelGCThreads=16 -Xmx16g -jar /usr/local/packages/VarScan/2.3.6/VarScan.jar somatic normal-tumor.pileup sample.out --output-vcf 1 --mpileup 1

It runs until the following and then stops.

Min coverage:   8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2:   1
Min var freq:   0.2
Min freq for hom:   0.75
Normal purity:  1.0
Tumor purity:   1.0
Min avg qual:   15
P-value thresh: 0.99
Somatic p-value:    0.05

Reading input from normal-tumor.pileup

Reading mpileup input...
Parsing Exception on line:
chr1    10154   C   2   a.  0;  0

Do you know what I'm doing wrong?


Entering edit mode

There are a couple of hits if you search "varscan mpileup parsing exception", seems like varscan is kinda picky about the version of samtools that you use. You might have to post on sourceforge to get this fixed


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