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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Incorrect path alignment #91

Open tobiasrausch opened 1 year ago

tobiasrausch commented 1 year ago

Hi Heng,

Extracting a chm13 subsequence and aligning it back to the pre-built graph results in an incorrect path alignment (deviating from rank 0 nodes) with lots of small InDels:

gfatools gfa2fa -s -0 chm13-90c.r518.gfa.gz > chm13.fa
samtools faidx chm13.fa chr1:1025000-1035000 > read.fa
minigraph --vc -k 15 -w 10 -t 24 -cx lr chm13-90c.r518.gfa.gz read.fa

This subsequence is uniquely mappable in chm13 using minimap2 at MAPQ 60.

Thanks, Tobias