HLA contigs causing errors with g2gtools patch and g2gtools transform

[jon4thin]

I have been trying to run g2gtools patch and g2gtools transform but encounter errors like:

[g2gtools] Error: invalid literal for int() with base 10: '02N' [g2gtools] Error: invalid literal for int() with base 10: '11N'

When I look at my VCI I see

##CONTIG=HLA-A*01:01:01:02N:3291
##CONTIG=HLA-A*01:11N:3374

and many others....

I removed the HLA contigs from the VCI for g2gtools patch but this is suboptimal for a couple reasons:

• Not the intended pipeline

• If I feed this to the next step, g2gtools transform, i get the error: [g2gtools] Error: Cannot parse location 'HLA-A*01:01:01:01:1-3503'

• I will later need to reintroduce these regions before alignment, they cant be left out completely.

Thank you!

[jon4thin]

This may be an issue with my g2gtools version. I am using the docker image: kbchoi/emase:latest