Problem using CNVkit with RNA-Seq Data to call CNV with Ensembl GRCh37 v75 annotation file

Question

[lumal29]

Hi everyone,

I want to use CNVkit to call CNVs on RNA-Seq data and I have to use an annotation file from Biomart to use import-rna. As I understood in the doc and in the file rna.py , this file need the following columns:

# "Gene stable ID" -- Ensembl ID
# "Gene % GC content"
# "Chromosome/scaffold name"
# "Gene start (bp)"
# "Gene end (bp)"
# "Gene name"
# "NCBI gene ID"
# "Transcript length (including UTRs and CDS)"
# "Transcript support level (TSL)"

The problem is that I need to use the version GRCh37 v75 of Biomart and the two last columns (Transcript length and TSL) are not available.

Is there a way to use CNVkit without those columns and if I really need them, where can I find this information?

Thank you very much

[lumal29]

As I didn't get any answer, I decided to use the last gtf version of GRCh37 to remake the count files with htseqcount (one of the input for CNVkit) and used the last version too on Biomart to make the annotation file. This version also doesn't have the TLS information though, but I saw this post which allowed me to find the TSL and I added it with the annotation file. Hope it will help someone.