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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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fetch called on bamfile without index? #29

Closed yebinkim17 closed 2 years ago

yebinkim17 commented 2 years ago

Hi, I enjoyed your article very much. Now I am trying to apply Cyrius software tool on analyzing CYP2D6 gene for my research. However, while I was trying to run the tool, I faced an error that I cannot figure out.

The command I entered is as following :

python3 star_caller.py --manifest manifest.txt --genome 38 --prefix test --outDir ./output/

This is the error I see:

ValueError: fetch called on bamfile without index

image

I don't think I need bam.bai file, but the error says that "could not retrieve index for bam file". (In the manifest.txt file, there is only one line of the bam file path.) So, I am wondering how I can troubleshoot this issue.

Also, can we use a sliced WGS bam file as an input? For example, ch22.bam.

Thank you very much.

xiao-chen-xc commented 2 years ago

Hi @yebinkim17, no need to put a bai file path in the manifest, but there should be a bai file in the same directory as the bam file. If you want to slice a WGS bam, please slice the regions specified in https://github.com/Illumina/Cyrius/blob/master/data/CYP2D6_region_38.bed

yebinkim17 commented 2 years ago

Thank you for your response. It resolved the issue.