Hi. I'm trying to run a sequenza with the output of varscan2 I used VarScan version of 2.4.3 and put into sequenza but I got an error message
"Error in data.frame(chromosome = as.character(varscan.somatic$chrom), : arguments imply differing number of rows: 0, 1"
This is my output of varscan
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr1 69511 . A G . PASS DP=116;SS=1;SSC=0;GPV=2.7689E-69;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:42:0:42:100%:0,0,37,5 1/1:.:74:0:74:100%:0,0,68,6
chr1 185795 . G T . PASS DP=8;SS=1;SSC=0;GPV=3.8462E-2;SPV=9.2857E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:3:1:2:66.67%:1,0,2,0 0/1:.:5:3:2:40%:3,0,2,0
chr1 629906 . C T . PASS DP=6;SS=1;SSC=0;GPV=1.0823E-3;SPV=1E0 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:3:0:3:100%:0,0,3,0 1/1:.:3:0:3:100%:0,0,3,0
and this is the argument for run sequenza
library("sequenza")
snp <- read.table("/DASstorage6/binnie/varscan/Somatic/filter_output/merge_1.Somatic.hc.filtered.vcf", sep="\t")
names(snp) = c("chrom", "POS", "ID", "ref", "var", "QUAL", "FILTER", "INFO", "FORMAT", "NORMAL", "TUMOR")
cnv <- read.table("/DASstorage6/binnie/varscan/copynumber/copy_2.copynumber", header=TRUE, sep="\t")
seqz.data <- VarScan2seqz(varscan.somatic = snp, varscan.copynumber = cnv)
My data has chromosome 1 to 22 and X,Y and also I ordered it as chromosome and position. I have no idea how can I fix this error. Could anyone give me some tip?
Did you guys solved the problem? I'm starting using sequenza and get into the same errors!