I'm running GISTIC2 on Sequenza generated segmentation data from whole exome tumor-normal pairs. I keep encountering the following warning:
Warning: markers on largest gene exceed markers on smallest chromosome: overriding gene-gistic > In gene_score_permutations at 43 In compute_stats at 83 In run_focal_gistic at 201 In run_gistic20 at 124 In run_gistic2_from_seg at 249 In gp_gistic2_from_seg at 97
I'm not really sure what this warning means and if I should be concerned about it affecting my results. According to the GISTIC documentation, the gene-gistic option "calculates the significance of deletions at a gene level instead of a marker level". What effect will this have on my results and should I be concerned?
Here is my GISTIC command:
./gistic2 -b $basedir \ -seg $segfile \ -refgene $refgenefile \ -ta 0.1 \ -armpeel 1 \ -brlen 0.7 \ -cap 1.5 \ -conf 0.90 \ -td 0.1 \ -genegistic 1 \ -gcm extreme \ -js 4 \ -maxseg 2000 \ -qvt 0.25 \ -rx 0 \ -savegene 1 \