baezortega / somatypus Goto Github PK

Hi,
I encountered an issue using Somatypus in the genotyping stage.

(8) PREPARING DATA FOR VARIANT GENOTYPING
Traceback (most recent call last):
File "/hgsccl/next-gen/scratch/chander/software/somatypus/src/Somatypus_ExtractRegions.py", line 138, in

start = int(exonComp[1].split('-')[0])
IndexError: list index out of range

ERROR: Output file /hgsccl/next-gen/scratch/chander/somatypus_out/8-18_genotyped/was not correctly generated. Please check the logs folder for more information.

Any thoughts why this error occurs?

Best,
Varuna

Yo man, your tool here is nice - but I can no longer accept the discriminatory nature of your code against organisms with large chromosomes!

I mean really large chromosomes, larger than yours. Think about marsupials, for example. Plants, big genome plants. Or what would the Marbled lungfish say if you can't run somatypus on him? "Speciesism!"

CSI indexing on VCFs and BAM files is the future, I tell ya bro. Check out my brand new golden changes to your core bash script, here attached.

No questions. Peace out.

somatypus_1.3_big_chromosomes.zip