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License: Other
Identification of structural variations
License: Other
Hello
i run vaquita on NGS bam file ,and it take two days and still running.
command like this:
vaquita call -r {ref} {bam} >{dir}/vaquita.vcf
i test ,if i use bam file alignment on GRC38 ref,it will take too long time. if i use hg19,it work well so far .
Do u have any idea?
I think now that SeqAn3 is officially out, we can start looking at converting to it.
I've started on my own fork and have already converted the Argument Parser and added seqan3 as a submodule.
Is there anything vaquita uses in seqan2 that is not yet in seqan3?
and change the readme.md
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.
The current version is slightly modified version of SeqAn regarding BAM I/O.
This modification resolves
So .. discuss this with Rene first
Currently, if there isn't a BAI file, vaquita will run all the way through and then exit on a segfault. It would be less confusing if this is checked for at the very beginning and the program interrupts.
Hi Jongkyu,
when I run Vaquita:
vaquita -cg hg19.fa input.bam > output.vcf
I'm getting the following exception:
[2017-3-2 15:15:51] [START] Split-read analysis
[2017-3-2 15:15:57] [END] Split-read analysis (6 seconds.)
[2017-3-2 15:15:57] [START] Paired-end analysis
[2017-3-2 15:15:57] [END] Paired-end analysis (0 seconds.)
[2017-3-2 15:15:57] [START] Clipped-read analysis
[2017-3-2 15:15:57] [END] Clipped-read analysis (0 seconds.)
[2017-3-2 15:15:57] [END] BREAKPOINT IDENTIFICATION (0 seconds.)
[2017-3-2 15:15:57] Found breakpoints
[2017-3-2 15:15:57] 24428 from split-read evidences.
[2017-3-2 15:15:57] 0 from read-pair evidences.
[2017-3-2 15:15:57] 1708878 from soft-clipped evidences.
[2017-3-2 15:15:57] [START] BREAKPOINT MERGING
[2017-3-2 15:15:57] [START] From split-read evidences.
[2017-3-2 15:15:57] [END] From split-read evidences. (0 seconds.)
[2017-3-2 15:15:57] [START] From read-pair evidences.
[2017-3-2 15:15:57] [END] From read-pair evidences. (0 seconds.)
[2017-3-2 15:15:57] [START] From soft-clipped evidences.
terminate called after throwing an instance of 'seqan::UnexpectedEnd'
what(): Unexpected end of input.
Aborted
I already tried with different input files and recreated hg19.fa.fai but all with the same result. Any idea why this is happening? ๐
.. need this function.
Considers HPC(including Xeon-Phi) environment, too
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