Min coverage: 10
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
Min avg qual: 15
P-value thresh: 0.1
Reading input from VariantsCalling/1.varScan.snp
Chrom Position Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-:pval SamplesRef SamplesHet SamplesHom SamplesNC Cons:Cov:Reads1:Reads2:Freq:P-value
Parsing Exception on line:
chr10 12258038 C T T:49:0:49:100%:3.925E-29 Pass:0:0:17:32:1E0 0 0 1 0 T:49:0:49:100%:3.925E-29
For input string: "T:49:0:49:100%:3.925E-29"
Parsing Exception on line:
chr10 24381890 T G G:10:0:10:100%:5.4125E-6 Pass:0:0:0:10:1E0 0 0 1 0 G:10:0:10:100%:5.4125E-6
For input string: "G:10:0:10:100%:5.4125E-6"
Parsing Exception on line:
chr10 26931820 C G G:48:0:48:100%:1.554E-28 Pass:0:0:38:10:1E0 0 0 1 0 G:48:0:48:100%:1.554E-28
For input string: "G:48:0:48:100%:1.554E-28"
Parsing Exception on line:
chr10 42135550 G T T:11:0:11:100%:1.4176E-6 Pass:0:0:2:9:1E0 0 0 1 0 T:11:0:11:100%:1.4176E-6
For input string: "T:11:0:11:100%:1.4176E-6"
Parsing Exception on line:
chr10 55848987 C G S:56:43:13:23.21%:5.5625E-5 Pass:0.0:39:4:0:13:1.2593E-9 0 1 0 0 S:56:43:13:23.21%:5.5625E-5
For input string: "S:56:43:13:23.21%:5.5625E-5"
Too many parsing exceptions encountered; exiting
I'm trying to filter a snp file using the command
But I encounter the error
any ideas, what I'm doing wrong?
thanks