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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg alignments not reporting split reads #4275

Open TammushB opened 2 months ago

TammushB commented 2 months ago

1. What were you trying to do? looking for split reads (supplementary alignments).

2. What did you want to happen? view split reads.

3. What actually happened? no supplementary alignments are reported after vg alignment. instead of split reads we see soft clip.

5. What data and command can the vg dev team use to make the problem happen? s3://ultimagen-april-2024-somatic/cram_files/031865-Lb_2211-Z0048-CTGCCAGACTGTGAT.cram

6. What does running vg version say? vg version v1.45.0-105-gd213c299c "Alpicella" Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux Linked against libstd++ 20210601 Built by root@69ed1be6e09d

jeizenga commented 2 months ago

You are correct, this is a capability that the aligners in vg do not have. It would be a valuable addition, but I don't know of any near-term plans to implement split-read alignment.