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Meta-information in output-vcf of VarScan looks not perfect. 1. "DP4" in FORMAT is : **##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">** It should be: **##FORMAT=<ID=DP4,Number=4,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">** right? This could raise errors subsequent analysis. 2. GT representation in VCF CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR` chr1 39423 . T C . PASS DP=37;SOMATIC;SS=2;SSC=4;GPV=1E0;SPV=3.2213E-1...

Meta-information in output-vcf of VarScan looks not perfect. 1. "DP4" in FORMAT is : **##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">** It should be: **##FORMAT=<ID=DP4,Number=4,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">** right? This could raise errors subsequent analysis. GT representation in VCF CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR` chr1 39423 . T C . PASS DP=37;SOMATIC;SS=2;SSC=4;GPV=1E0;SPV=3.2213E-1...

Hi, Arshi. I happened to run oncotator with VCF file generated from Varscan and strelka. Athough the website (http://portals.broadinstitute.org/oncotator/help/#inputformat) requires the input file containing only 5 columns, I run the commond line in shell "oncotator -v -i VCF -o TCGAMAF --db-dir=oncotator_v1_ds_April052016 -c tx_exact_uniprot_matches.txt --override_config overrides.config sample-0001.indel.vcf sample.indel.oncotator.maf hg19 " .Get the output TCGAMAF file and it looks good! So what...

Hello, Dan! Thanks a lot! But I get confused by the "readcount" file. I get a position file following your advice.Then I run two tools to generate readcounts file: bam-readcount and VarScan-readcounts with the same patameters "-q 20 -w 1". Which troubles me is there is a huge differecne between the both results by the two tools. Especially the readcounts file is empty from VarScan-readcounts. I just cann't find why this happens by now. The command I run is as follows: java -jar VarScan.v2.3.9.jar...

VarScan version I use is 2.3.9. I run the workflow like this: VarScan-somatic first,...