Comments (2)
Thank you Josh
Sorry for the late reply.
I'm back to this project and will look into your case.
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@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.
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Related Issues (15)
- Better .vcf outputs.
- Adding test cases
- Connect with Travis for CI HOT 1
- Set user group / mailing lists
- Better packaging
- Build binaries for other OS HOT 1
- Refactoring for multi-threading HOT 1
- Use new SeqAn library
- seqan::UnexpectedEnd HOT 3
- Multisample genotpying. HOT 1
- Don't segfault when no bam index file exists.
- Converting to seqan3
- q
- take too much time to run vaquita
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