Doesn't seem to be working properly on long reads.

[joshuak94]

Tested with the following: --no-pe, --no-re, -c 2, -q 10 on NA12878 sequenced with Pacbio, aligned with NGMLR, using hg19 as a reference. Results in empty VCF file.

[xenigmax]

Thank you Josh

Sorry for the late reply.
I'm back to this project and will look into your case.

[joshuak94]

@xenigmax Quick update.

I ran vaquita as follows:

bin/vaquita --no-pe --no-re -c 2 -q 10 -r /group/ag_abi/takifugu-data/SeqAn/homo_sapiens/NA12878/NA12878_pacbio_blasr.bam

The issue is I only get a very small number of SVs, and they're only deletions...

[2019-9-20 15:4:59] Found evidences
[2019-9-20 15:4:59] 65431 from split-reads.
[2019-9-20 15:4:59] 0 from discordant read-pairs.
[2019-9-20 15:4:59] 35479923 from soft-clipped reads.
...
[2019-9-20 15:7:14] Found SVs
[2019-9-20 15:7:14] 1431 deletions.
[2019-9-20 15:7:14] 0 inversions.
[2019-9-20 15:7:14] 0 duplications.
[2019-9-20 15:7:14] 0 translocations.