Empty snv.tsv and indel.tsv files about docker-bam_readcount_helper-cwl HOT 9 OPEN

Can you please attach your input VCF for further debugging on our end?

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I am attaching a shortened version of my original VCF file here for debugging.

example.vcf.zip

from docker-bam_readcount_helper-cwl.

Hi @susannasiebert, any updates on this ? Please let me know if you need anything else from me. Thank you.

from docker-bam_readcount_helper-cwl.

I apologize but I've been absolutely swamped with other projects. I will be on vacation this week but will look into it when I get back.

from docker-bam_readcount_helper-cwl.

Thanks for the update. Enjoy your time off :)

from docker-bam_readcount_helper-cwl.

I dug into this and from what I can tell it does generate region lists for the SNPs in your file (those files are tmp files so you won't see them as an output). If the final output files are empty, this usually means that those positions are low quality. You could try investigating these positions in IGV and/or adjusting the min_base_quality and and min_mapping_quality parameters. Are you seeing this issue for both samples?

from docker-bam_readcount_helper-cwl.

Hi @susannasiebert, thanks for looking into this. I needed some clarification on your suggestion:

1. Which positions should I look at in IGV ? I don't see the region lists so I don't know what to focus on
2. At which step should I adjust the min_base_quality and and min_mapping_quality parameters ?

I tried this on multiple VCFs and I'm getting the same issue.

from docker-bam_readcount_helper-cwl.

1. I have attached the region lists for your VCF.
   region_files.zip

2. The min_base_quality and the min_mapping_quality are optional parameters to the bam_readcount_helper.py script (last two positional parameters, in that order).

If you are having problems with all of your VCFs, that's indeed concerning. Without having access to your bams or the reference fasta you chose, I can't really debug it on my end. I would also need some more information on how precisely you are running things on your end.

from docker-bam_readcount_helper-cwl.

Thanks for sending these. I’ll do a little investigation on my end and get back to you by the end of the week. Thanks for your help.

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