Entering edit mode
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