Matlab step error in RNA-mutect pipeline

Question

[agoel]

Hi,

I am trying to run RNA-Mutect and have reached the filtering step (step 2 in the Readme). This step involves calling matlab binary script file and I am repeatedly getting the error detailed below. Hoping to resolve this, I have tried these steps already -

1) Using the pass calls only in the Mutect vcf to arrive at the MAF (from vcf2maf). Also filtering the mutect call stats file to retain lines only for the pass calls. 2) Retaining or removing alternate contigs (like GL00*) and MT, chrX and chrY. 3) Switching the chromosome name style from "1" to "chr1" 4) Have also tried the various ver./ uploads of the script at Zenodo (here)

and, finally I have also tried the example output provided from Step 1 to test and receive the same error message.

My command setup (HPC environ, with RNA-mutect being loaded via module load)

run_FilterRNAMutationsNoPoN.sh \
/path/to/MCR/R2016a/v901 \
tum-normal_pair_ID \
Tum.maf \
mutect_call_stats.out \
MIN_ALT_COUNT=3 \
path/to/RNA_MUTECT/1.0-foss-2019a/mat_files/Darned_mat.mat \
path/to/RNA_MUTECT/1.0-foss-2019a/mat_files/Radar_mat.mat \
path/to/RNA_MUTECT/1.0-foss-2019a/mat_files/Exac_mat.mat

And the error I am getting whatever I try -

Error using >=
Matrix dimensions must agree.

Error in FilterRNAMutationsNoPoN (line 21)

MATLAB:dimagree

Any suggestions if you have been able to run this successfully would be much appreciated. The same error message has been posted by an user in the Github repo. (here) but that hasn't received any response yet. I can of course not look at what is at line 21 of the script as it is a binary file.

[ATpoint]

There does not seem to be any dynamic in the GitHub issues, nor in the commits. Either see if you can email them or simply switch tools.

[agoel]

Thanks, I will drop an email after waiting a bit more. and I will also try if I can implement the filtering steps on my own, though even if I succeed I won't be able to say I used RNA-mutect technically as the actual implementation is hidden to me in the binary script. I will make an effort though as at moment this is the only tool (for somatic mut. from RNA) to have gained recognition in a reputed journal.