Question: converting varscan2 output to sequenza
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gravatar for a01039012387
20 months ago by
a0103901238710
a0103901238710 wrote:

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?

snp mutation wes exome • 984 views
ADD COMMENTlink modified 14 months ago by nilesh.gardi26880 • written 20 months ago by a0103901238710
0
gravatar for nilesh.gardi2688
14 months ago by
nilesh.gardi26880 wrote:

Is problem get solved? I am also getting similar error as follows:

Error: Error in [.data.frame(varscan.somatic, idx, c("ref", "var")) : undefined columns selected

I am using ##fileformat=VCFv4.1 as input. Please help.

ADD COMMENTlink written 14 months ago by nilesh.gardi26880
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