Does VarScan output work with NGS Benchmarking v1.6.?
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2.6 years ago
ManuelDB ▴ 110

How can I generate a VCF file using VarScan? I need this format to check the sensitivity and specificity after running NGS Benchmarking v1.6.

The documentation says that the option --output-vcf should do that but the output I get looks like this

 Chrom   Position        Ref     Cons    Reads1  Reads2  VarFreq Strands1        Strands2        Qual1   Qual2   Pvalue  MapQual1
        MapQual2        Reads1Plus      Reads1Minus     Reads2Plus      Reads2Minus     VarAllele 1       12198   G       S       9       8   
47.06%  2       2       54      56      0.98    1       1       5       4       3
       5       C 1       13302   C       Y       6       8       57.14%  2       2       45      41      0.98    1       1       2       4       4

Am I doing something wrong (most likely) or is this what they call VCF format?

My full code

 java -jar VarScan.v2.4.2.jar pileup2snp /mainfs/wrgl/NA12878-data/NA12878/NA.mpileup --output-vcf    > ./NA_snp.VCF
VarScan NGS_Benchmarking • 424 views
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