Procedure to run OptiType for HLA Typing a BAM File

Question

[Umesh]

Complete newbie here.

Got BAM File from Dante Labs.

Want to do HLA Typing of my BAM

Installed Optitype using Conda.on Ubuntu installation on Windows.

My BAM Stored in D Drive as sample.bam

Do I need a reference genome file and any other repositories before analysing my sample?

Currently I am at (base) umesh@umesh-PC:~$

Could someone kindly guide me how to proceed. Many Thanks.

[swbarnes2]

Are you completely sure that this software takes bam files as input?

[Umesh]

I guess so. On the github page, it says that .bam files can be used as input.

Blockquote if you want to re-run OptiType on the same sample, you can give it those intermediate .bam files as input instead of .fastq files, and spare on the mapping part of the pipeline. Note: these .bam files have nothing to do with those produced during the filtering/fishing step. Blockquote

https://github.com/FRED-2/OptiType

[swbarnes2]

So your bam is an intermediate output of optitype?

[Umesh]

No, my BAM is the full BAM file we get after the WGS 30x test. But my point was that the software seems capable of analysing BAM files, so probably it should work on my BAM for HLA typing. I hope I find someone who has done HLA typing on BAM coz it doesn't seem to be commonly done. Thanks for your prompt replies.

[Umesh]

No, my BAM is the full BAM file we get after the WGS 30x test. But my point was that the software seems capable of analysing BAM files, so probably it should work on my BAM for HLA typing. I hope I find someone who has done HLA typing on BAM coz it doesn't seem to be commonly done. Thanks for your prompt replies.

[Jingjingzhang]

Hi, I encountered the similar question with you. Do you try the test data on github(https://github.com/FRED-2/OptiType)？ I can't run it successfully.