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Illumina / DRAGMAP

DRAGEN open-source mapper
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Reporting all alignments #15

Open donovan-h-parks opened 2 years ago

donovan-h-parks commented 2 years ago

Hi,

Is it possible to have DRAGMAP report all alignments similar to BWA-MEM with the -a option? This seems possible with the different sec parameters, but I have not been able to get more than a single alignment reported. I have a simple test case where the reference DB contains two identical sequences and the query reads have 100% identity to these reference sequences. As such, I'm expecting to see two mappings (at 100% identity) to each of the reference sequences when using something like:

dragen-os -r ./dragmap_db -1 query.fq --Aligner.sec-aligns 10  --Aligner.sec-phred-delta 10  --Aligner.sec-score-delta 10

Any insights you can provide would be much appreciated.

Thanks, Donovan

rpetrovski commented 2 years ago

I don't see anything particularly wrong with your command line. Would you be able to share the sequences and the reference?

donovan-h-parks commented 2 years ago

Hello. Thank you for the quick response. I've attached the files. I needed to compress them for GitHub to accept the files.

ref.fna.gz query.fq.gz

rpetrovski commented 2 years ago

It seems the issue is caused by your reference being too short. This is a bug with dragmap. When I append your reference to human genome, the alignment works as expected. I will be able to have a closer look next week.

R.