Error "Bad formatting for indel alleles: cct_C" when runnning cortex_var

[Daniel Cameron]

I'm running cortex_var on some simulated data using the quick start documentation (using k31 only to speed up processing) and the comversion of the PD to VCF appears to have failed on the fourth variant call. Given the error message:

Bad formatting for indel alleles: cct_C at ~/tools/cortex/CORTEX_release_v1.0.5.21//scripts/analyse_variants/process_calls.pl line 2068, <$fh_proc_bub> line 36.

and the relevant code in process_calls.pl, it appears that cortex requires fully uppercase reference genome due to the case sensitive regexes used. This seems at odds with other cortex code such as the process_call.pl rev_comp which does allow for both upper and lower case bases.

Is this behaviour considered a bug, do I need to change the casing on my reference, or have I misinterpreted the error?

Thanks

Daniel Cameron

[Zamin Iqbal]

Daniel

Bad formatting for indel alleles: cct_C at ~/tools/cortex/CORTEX_release_v1.0.5.21//scripts/analyse_variants/process_calls.pl line 2068, <$fh_proc_bub> line 36.

and the relevant code in process_calls.pl, it appears that cortex requires fully uppercase reference genome due to the case sensitive regexes used. This seems at odds with other cortex code such as the process_call.pl rev_comp which does allow for both upper and lower case bases.

Is this behaviour considered a bug, do I need to change the casing on my reference, or have I misinterpreted the error?

I consider this a bug. Please raise it as an issue here

https://github.com/iqbal-lab/cortex/issues

For now, a workaround is changing your reference to be upper case

Sorry!

Zam

 

Thanks

Daniel Cameron