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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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No result for hlacaller: optitype #3252

Closed rkendar closed 4 years ago

rkendar commented 4 years ago

Version info

Hi Bcbio Team,

Currently, I am running HLA typing using OptiType. I use BAM as input aligner: false, since I don't want to redo the mapping step to fasten the process. And I have specified hlacaller: [optitype] in my .yaml.

However, why it doesn't give me the output -hla-optitype.csv in my final/ or work/ ? I did see the message about HLA typing in debug.log as below:

[2020-05-30T14:04Z] Timing: hla typing
[2020-05-30T14:04Z] multiprocessing: call_hla

But I cannot find ant optitype command in command.log. Do you know what happens? Is it because I start the input using BAM instead of FASTQ? I have attached my .yaml. template. yaml.txt

Thank you!

chapmanb commented 4 years ago

Thanks for the question on HLA calling. You're exactly right that HLA calling is not available if you're not doing alignment as part of the run. When aligning, there is a bwa post-processing script that extracts HLA reads and then uses those as inputs for the calling process. You can start with bam files as inputs but will have to turn alignment on. Hope this helps.

rkendar commented 4 years ago

Hi @chapmanb @roryk ,

Thank you for your answer. I understand now. But, if I'm turning on the aligner aligner: bwa, will it raise any issue for other processes (like raise error since the input is BAM)? Because as you can see I have variantcaller and svcaller as well in my yaml file.

Thank you!

roryk commented 4 years ago

Hi @rkendar,

You can use a BAM file as input to bcbio and it will do the right thing for tools that need to start from FASTQ files so you should be all set.