I am applying Varscan filter to an output file from mpileup2snp and my commend line is
java -jar /risapps/rhel5/VarScan/2.3.7/VarScan.v2.3.7.jar filter snp/3559-T7.bin.align.sorted.snp --min-coverage 15 --min-var-freq 0.05 --output-file 3559-T7.bin.align.sorted.filtered.snp
I get the following error:
Min coverage: 15
Min reads2: 2
Min strands2: 1
Min var freq: 0.05
Min avg qual: 15
P-value thresh: 0.1
Reading input from snp/3559-T7.bin.align.sorted.snp
Parsing Exception on line:
chr1 4525626 T C C:10:0:10:100%:5.4125E-6 Pass:1.0:0:0:10:0:1.6254E-2 0 0 1 0 C:10:0:10:100%:5.4125E-6
For input string: "C:10:0:10:100%:5.4125E-6"
Parsing Exception on line:
chr1 4525643 T C C:9:0:9:100%:2.0568E-5 Pass:1.0:0:0:9:0:1.4706E-2 0 0 1 0 C:9:0:9:100%:2.0568E-5
For input string: "C:9:0:9:100%:2.0568E-5"
Parsing Exception on line:
chr1 4688049 T C C:20:0:20:100%:7.2544E-12 Pass:0:0:16:4:1E0 0 0 1 0 C:20:0:20:100%:7.2544E-12
For input string: "C:20:0:20:100%:7.2544E-12"
Parsing Exception on line:
chr1 4688069 T C C:10:0:10:100%:5.4125E-6 Pass:0:0:9:1:1E0 0 0 1 0 C:10:0:10:100%:5.4125E-6
For input string: "C:10:0:10:100%:5.4125E-6"
Parsing Exception on line:
chr1 4688141 T C C:17:0:17:100%:4.2852E-10 Pass:0:0:0:17:1E0 0 0 1 0 C:17:0:17:100%:4.2852E-10
For input string: "C:17:0:17:100%:4.2852E-10"
Too many parsing exceptions encountered; exiting
Does anyone know how I can solve this problem?
Thank you!
java -jar /risapps/rhel5/VarScan/2.3.7/VarScan.v2.3.7.jar filter snp/3559-T7.bin.align.sorted.snp --min-coverage 15 --min-var-freq 0.05 --output-file 3559-T7.bin.align.sorted.filtered.snp
I get the following error:
Min coverage: 15
Min reads2: 2
Min strands2: 1
Min var freq: 0.05
Min avg qual: 15
P-value thresh: 0.1
Reading input from snp/3559-T7.bin.align.sorted.snp
Parsing Exception on line:
chr1 4525626 T C C:10:0:10:100%:5.4125E-6 Pass:1.0:0:0:10:0:1.6254E-2 0 0 1 0 C:10:0:10:100%:5.4125E-6
For input string: "C:10:0:10:100%:5.4125E-6"
Parsing Exception on line:
chr1 4525643 T C C:9:0:9:100%:2.0568E-5 Pass:1.0:0:0:9:0:1.4706E-2 0 0 1 0 C:9:0:9:100%:2.0568E-5
For input string: "C:9:0:9:100%:2.0568E-5"
Parsing Exception on line:
chr1 4688049 T C C:20:0:20:100%:7.2544E-12 Pass:0:0:16:4:1E0 0 0 1 0 C:20:0:20:100%:7.2544E-12
For input string: "C:20:0:20:100%:7.2544E-12"
Parsing Exception on line:
chr1 4688069 T C C:10:0:10:100%:5.4125E-6 Pass:0:0:9:1:1E0 0 0 1 0 C:10:0:10:100%:5.4125E-6
For input string: "C:10:0:10:100%:5.4125E-6"
Parsing Exception on line:
chr1 4688141 T C C:17:0:17:100%:4.2852E-10 Pass:0:0:0:17:1E0 0 0 1 0 C:17:0:17:100%:4.2852E-10
For input string: "C:17:0:17:100%:4.2852E-10"
Too many parsing exceptions encountered; exiting
Does anyone know how I can solve this problem?
Thank you!