Comments (5)
@inti I think this should be possible by annotating paths in the graph. These paths can be used to project alignments (vg surject
) against the graph against a particular path. This subgraph could be a personal genome. Does this make sense?
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Yes, it does make sense. I just have not got chance to try it. I will have a chance soonish. Cheers, Inti
On Jul 13, 2015, at 08:38, Erik Garrison [email protected] wrote:
@inti https://github.com/inti I think this should be possible by annotating paths in the graph. These paths can be used to project alignments (vg surject) against the graph against a particular path. This subgraph could be a personal genome. Does this make sense?
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Reply to this email directly or view it on GitHub #40 (comment).
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I'm going to close this because, while it's a cool project, it's not really a vg bug.
from vg.
Hey @inti , if you've tried it out let us know - we'd like to hear a success story if you have one, and you can catch us on gitter if for some reason things didn't work!
from vg.
Thanks. I will try to get around to test it and I will let you know. Cheers, Inti
On Sep 21, 2016, at 05:03, Eric T. Dawson [email protected] wrote:
Hey @inti https://github.com/inti , if you've tried it out let us know - we'd like to hear a success story if you have one, and you can catch us on gitter https://gitter.im/vgteam/vg if for some reason things didn't work!
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Related Issues (20)
- Program stuck at [IndexRegistry]: Chunking VCF(s) for days HOT 2
- vg alignments not reporting split reads HOT 1
- Mapping paired end reads with vg giraffe: "Falling back on single-end mapping" HOT 9
- Autoindex should parse tabix-indexed monolithic VCFs in parallel
- vg pack error HOT 3
- VCF file empty when calling SV on ONT data HOT 9
- vg map errors HOT 5
- Genotyping SVs in a minigraph-cactus graph yields many similar alleles in output vcf HOT 1
- How to align both long and paired end short reads using vg HOT 1
- Augmentation failed on one chromosome, but succesfull on other chromosomes HOT 3
- Can VG simulate the third-generations long reads? HOT 5
- Issue with vg map and vg augment for certain inputs. HOT 2
- Merging multiple graph files HOT 4
- short read giraffe alignment crashes most of the time, works on a few random samples - Signal 11 HOT 2
- Running VG deconstruct failed in the gfa generated from PGGB pipline HOT 3
- ERROR vg autoindex :Tag "transcript_id" not found in attributes (line 145). ERROR: Tag "transcript_id" not found in attributes (line 4). ERROR: No transcripts parsed (remember to set feature type "-y" in vg rna or "-f" in vg autoindex) HOT 1
- Error Exceeded Limit of Size on Disk While Running vg index HOT 1
- Mapping paired reads w/ giraffe, no EOF marker, job stalls, exit code 79 HOT 5
- Construct a generation-level pan-genome HOT 5
- Release vg v1.58.0
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