Error in perform Ziggurat deconstruction

[Elena Lara]

Hello,

I am trying to run GISTIC on a segments file but can't seem to solve an error.

GISTIC version: v.2.0.23

Input file: segments file from WGS, with columns patient, analysis, chromosome, cnv_start, cnv_end, median_coverage, median_baf_logodds, n_hetero_snps, total_snps, major_copy_number, minor_copy_number, gain_loss and loh. I am not sure which pipeline was used to create this file. Also, I am using the columns n_hetero_snps as "Num markers" and median_baf_logodds as "Seg.CN"

Genome version: hg19

The rest of parameters are left as default.

The error is:

Index exceeds matrix dimensions.

Error in normalize_by_arm_length (line 85)

Error in make_sample_B (line 50)

Error in perform_deconstruction (line 68)

Error in perform_ziggurat_deconstruction (line 126)

Error in run_focal_gistic (line 151)

Error in run_gistic20 (line 124)

Error in run_gistic2_from_seg (line 249)

Error in gp_gistic2_from_seg (line 97)

We have tried as well filling the gaps between segments and creating our own markers file, but the same error remains. 

Hope you can help us!

Best,

Elena.

[Barbara Hill]

Hello Elena,

For an error like this, it is best to post in the GISTIC Forum, where the lead developer and other members of the GISTIC community can assist you. 

In this case, there are many instances of this error and this post may be of help.

Best

-Barbara

[Elena Lara]

Thank you, Barbara.

I moved the question to https://groups.google.com/a/broadinstitute.org/g/gistic-forum/c/dcdJvGu-WBw/

Best,

Elena.