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vgteam
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vg
tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Align transcriptome data to an already-constructed pangenome graph
#4322
CarlosAmadeo7
opened
1 hour ago
0
vg giraffe mapping slow when vg autoindex return a waring `distance index uses oversized snarls, which may make mapping slow`
#4321
Wenhai-Zhang
opened
14 hours ago
0
Fix misplaced indel edits
#4320
adamnovak
closed
2 days ago
1
Make vg inject use AlignmentEmitter and support GAF
#4319
adamnovak
opened
3 days ago
0
error:[vg::Constructor] Variant/reference sequence mismatch
#4318
peanut-nu
opened
3 days ago
0
About vg call -a -A
#4317
JiadongZHONG
closed
2 days ago
1
Pad out fallback pair alignments
#4316
adamnovak
opened
4 days ago
0
Giraffe can crash when multi-mapping paired-end reads without a fragment lenght distribution
#4315
adamnovak
opened
4 days ago
0
Don't output VCF lines larger than 2Gi
#4314
glennhickey
closed
4 days ago
0
Do not convert multiple ref alleles with deconstruct -n
#4313
glennhickey
closed
4 days ago
0
check zstdlib error codes in vcf writer
#4312
glennhickey
closed
4 days ago
0
Faster surject for long and short reads with GBZ
#4311
jeizenga
closed
2 weeks ago
0
Port `vg filter --exact-name` from lr-giraffe branch
#4310
adamnovak
closed
2 weeks 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
3 weeks ago
0
vg pack signal 6 error
#4307
vetsuisse-unibe
opened
3 weeks ago
3
How to quantify the uncore gene expression by using vg rna
#4306
HanYu-me
closed
3 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
4 weeks ago
0
VG autoindex not working with PGGB GFA
#4302
KopalliV
opened
1 month ago
3
Deconstruct option to cluster similar alleles together
#4301
glennhickey
closed
1 month 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
2 months ago
5
VCF file empty when calling SV on ONT data
#4279
SwenDiepstraten
opened
2 months 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
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