Entering edit mode
9.9 years ago
Jordan
★
1.3k
Hi,
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!
I did what was suggested. I have a new problem now. There are no variants being generated.
I used the following code:
It runs until the following and then stops.
Do you know what I'm doing wrong?
Thanks!
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