dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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filtering error - "Too many parsing exceptions encountered" #51

Open yeroslaviz opened 4 years ago

yeroslaviz commented 4 years ago

I'm trying to filter a snp file using the command

 java -jar ~/VarScan.v2.3.9.jar filter  VariantsCalling/1.varScan.snp –-indel-file VariantsCalling/1.varScan.indel –-output-file VariantsCalling/1.varScan.filtered.snp

But I encounter the error

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

any ideas, what I'm doing wrong?

thanks

JessBuddle commented 2 years ago

Im having same issue - was this ever solved? Thanks!