Error in running Viscap

[luckyluke95]

Dear all,

I want to use VisCap for my run but I have the following error message :

[1] "./coverage_files/run_11.sample_interval_summary"
Error in matrix(tab[, col_name], dimnames = list(rownames(tab), new_head)) : 
 length of 'dimnames' [1] not equal to array extent
Calls: make_matrix_from_cov_files -> matrix
Exécution arrêtée

I have generated correct output files (I think...) from GATK v.3.4 DepthOfCov but it seems that something is wrong and I really do not understand why... Here are my files from GATK_output :: run_11.zip

And here is my command line to run Viscap :

Rscript VisCap.R ./coverage_files output_viscap/ VisCap.cfg

and my VisCap.cfg and VisCap.R files VisCap.zip

Does anybody have an idea please ?

I don't know where to find test files (generated by GATK DepofCov, and bed file) in order to test if the problem does not come from my files...

Thank you in advance

[luckyluke95]

Ok I finally found where the error message comes from 👍 So we have to use input from GATK DepthOfCoverage but be sure that you do not create the coverage files at the same time with a .bam list of files : do not use ($GATK -I bam.list) but unique bam($GATK -I bam1, $GATK -I bam2...etc), one by one to create all the sample coverage files.

Previously, I used a unique .run_interval_summary harboring all the samples but when replacing it with separate .sample_interval_summary files, it works now.

Hope this help