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ITBE-Lab / MA

The Modular Aligner and The Modular SV Caller
MIT License
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Multiple identical alignments were produced in the output #16

Closed dawnmy closed 1 year ago

dawnmy commented 1 year ago

I noticed that sometimes, MA produces SAM file with the same alignment occurring multiple times on Nanopore data. They have the same read, ref contig, start pos, and even the cigar. The command line I used:

 maCMD -t 20 -x ma_db.json -p Nanopore -i barcode01.fq.gz -o barcode01.sam -s maxSpan -M 5 --Use_M_in_CIGAR false

One of the read have six the same alignment (only show read, ref_contig, pos):

185-b77e-25cb88888888    GCF_000182965.3|NC_032094.1       171367
185-b77e-25cb88888888    GCF_000182965.3|NC_032094.1       171367
185-b77e-25cb88888888    GCF_000182965.3|NC_032094.1       171367
185-b77e-25cb88888888    GCF_000182965.3|NC_032094.1       171367
185-b77e-25cb88888888    GCF_000182965.3|NC_032094.1       171367
185-b77e-25cb88888888    GCF_000182965.3|NC_032094.1       171367

I am using Version 1.1.4-d2d8fc1-0 installed with conda

Is this expected. What could be the reason causing this issue?

dawnmy commented 1 year ago

My bad, there are some duplicate sequences in the ref db.