vgteam vg issues - Githubissues

vgteam / vg

tools for working with genome variation graphs

https://biostars.org/tag/vg/

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Do not convert multiple ref alleles with deconstruct -n

#4313 glennhickey opened 2 hours ago
0
check zstdlib error codes in vcf writer

#4312 glennhickey opened 3 hours ago
0
Faster surject for long and short reads with GBZ

#4311 jeizenga closed 1 week ago
0
Port `vg filter --exact-name` from lr-giraffe branch

#4310 adamnovak closed 1 week ago
0
star allele toggle for deconstruct

#4309 glennhickey closed 2 weeks ago
0
Remove limit on Dozeu problem cell count from old Giraffe codepath

#4308 adamnovak opened 2 weeks ago
0
vg pack signal 6 error

#4307 vetsuisse-unibe opened 2 weeks ago
3
How to quantify the uncore gene expression by using vg rna

#4306 HanYu-me closed 2 weeks ago
1
vg augment forwardize_breakpoints error

#4305 genesok opened 3 weeks ago
1
More sophisticated nesting option for vg deconstruct

#4304 glennhickey closed 3 weeks ago
0
Fix command line downsmapling parameters to match what they're doing

#4303 xchang1 closed 3 weeks ago
0
VG autoindex not working with PGGB GFA

#4302 KopalliV opened 4 weeks ago
3
Deconstruct option to cluster similar alleles together

#4301 glennhickey closed 4 weeks ago
0
Pin back Requests to make sure Python Docker API works

#4300 adamnovak closed 1 month ago
0
Release vg v1.58.0

#4299 adamnovak opened 1 month ago
0
Refactor deconstruct to use less protobuf

#4298 glennhickey closed 1 month ago
0
Explain how to get vg on the PATH

#4297 adamnovak closed 1 month ago
0
Allow reading GAMs with embedded JSON metadata

#4296 adamnovak closed 1 month ago
0
Construct a generation-level pan-genome

#4295 jwli-code opened 1 month ago
5
Mapping paired reads w/ giraffe, no EOF marker, job stalls, exit code 79

#4294 AlphaJulietAlpha opened 1 month ago
5
Error Exceeded Limit of Size on Disk While Running vg index

#4293 AishaAlsuwaidi opened 1 month ago
1
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)

#4292 08li20 opened 1 month ago
1
Running VG deconstruct failed in the gfa generated from PGGB pipline

#4291 isaamael opened 1 month ago
3
short read giraffe alignment crashes most of the time, works on a few random samples - Signal 11

#4290 jespindel01 closed 1 month ago
2
Merging multiple graph files

#4289 Lucio-Yang opened 1 month ago
4
Issue with vg map and vg augment for certain inputs.

#4288 whelixw closed 1 month ago
2
Remove repetitive words

#4287 adamnovak closed 1 month ago
0
Annotate subpath

#4286 adamnovak closed 1 month ago
0
Make WFAExtender apply full length bonuses even though it doesn't use them internally

#4285 adamnovak closed 1 month ago
0
Can VG simulate the third-generations long reads?

#4284 tanger-code opened 1 month ago
5
Augmentation failed on one chromosome, but succesfull on other chromosomes

#4283 mas-agis opened 1 month ago
3
How to align both long and paired end short reads using vg

#4282 nathanLauHKGI closed 1 month ago
1
Genotyping SVs in a minigraph-cactus graph yields many similar alleles in output vcf

#4281 henrivkgt opened 1 month ago
1
vg map errors

#4280 santhanakrishnanb closed 1 month ago
5
VCF file empty when calling SV on ONT data

#4279 SwenDiepstraten opened 1 month ago
9
vg pack error

#4278 QiaoYJYJ opened 2 months ago
3
Autoindex should parse tabix-indexed monolithic VCFs in parallel

#4277 jeizenga opened 2 months ago
0
Mapping paired end reads with vg giraffe: "Falling back on single-end mapping"

#4276 evcurran opened 2 months ago
9
vg alignments not reporting split reads

#4275 TammushB opened 2 months ago
1
Program stuck at [IndexRegistry]: Chunking VCF(s) for days

#4274 Jokendo-collab opened 2 months ago
2
Merge of different chromosome graph files

#4273 Lucio-Yang closed 2 months ago
2
remove debug messages

#4272 glennhickey closed 1 month ago
0
a problem about vg autoidex (v1.56.0)

#4271 dongdongdong0203 opened 2 months ago
1
Hello, I want to get some information from Snarl file

#4270 pioneer-pi closed 1 month ago
1
Haplotype sampling example

#4269 jltsiren closed 2 months ago
0
Pad libdeflate for renaming on Mac

#4268 adamnovak closed 1 month ago
0
vg mpmap mapping reads to pan-transcriptom too slow

#4267 jkfo002 closed 2 months ago
8
Release vg v1.57.0

#4266 adamnovak closed 1 month ago
1
Add codenames

#4265 adamnovak closed 2 months ago
0
ERROR: Tag "transcript_id" not found in attributes (line 145).

#4264 08li20 opened 2 months ago
3