Hello,
VarScan team, I used VarScan to call snps from a pair of prostate cancer RNA-seq data in VCF format. The command line:
java -jar VarScan.v2.3.4.jar somatic ERR031017.pileup ERR031018.pileup --output-vcf 1 > ERR031018.VarScan.snp.vcf
The ERR031018.VarScan.snp.vcf only contains 26749 snps, however I tried the follwing command line before, the number of snps were 116392.
java -jar VarScan.v2.3.4.jar somatic ERR031017.pileup ERR031018.pileup ERR031018.VarScan.snp
I don't know why ? Thank you so much.
VarScan team, I used VarScan to call snps from a pair of prostate cancer RNA-seq data in VCF format. The command line:
java -jar VarScan.v2.3.4.jar somatic ERR031017.pileup ERR031018.pileup --output-vcf 1 > ERR031018.VarScan.snp.vcf
The ERR031018.VarScan.snp.vcf only contains 26749 snps, however I tried the follwing command line before, the number of snps were 116392.
java -jar VarScan.v2.3.4.jar somatic ERR031017.pileup ERR031018.pileup ERR031018.VarScan.snp
I don't know why ? Thank you so much.
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