VCF format of VarScan output

[LI Jia]

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.

[dkoboldt]

Hello, and thank you for your question. When you specify VCF output format, VarScan reports sites that failed its internal filters, such as the strand-filter, and this is indicated in the FILTER column. Otherwise, the default format does not report these. This should account for the difference.