Entering edit mode
2.8 years ago
tjbencomo
▴
50
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 \