GISTIC isn't checking chromosome 23 / X

Question

[penington.j]

Hi, I have a problem with GISTIC apparently not checking for CNV on chromosome X. GISTIC2 runs without errors on my segmentation file with the supplied reference file refgenefile=refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat

My input file has CNV events in chromosome '23' but the GISTIC run does not seem to be checking chromosome 23, even though I include option -rx 0

The outputs to stdout include Finding peaks on chromosome n for all n from 1-22, but not 23

I paste my run script below in case someone can see a problem with my switches Thanks, Jocelyn

segfile=f70psdwv6bfr2m399v6klvpz2900wv5j-bionix-facets_tcn2gistic.tsv
refgenefile=refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat

./gistic2 -b $basedir -seg $segfile -refgene $refgenefile  \
  -genegistic 1 -broad 1 -brlen 0.5 -twoside 1  \
  -conf 0.90 -rx 0 \
  -savegene 1 -gcm extreme  \
  -saveseg 0 -savedata 0

[penington.j]

Most of the switches are copied from the example documentation

Answer 1

[penington.j]

I found the answer. Four of my 133 samples had no entries in the segmentation file for chromosome 23.

When I added dummy entries so that all samples had all chromosomes, chromosome 23 / X was included in the output.