HKU-BAL Clair3 issues - Githubissues

HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

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empty vcf file

#297 DaliBAmor closed 7 months ago
3
Clair3 application

#296 QuentinPerriere closed 7 months ago
3
No module named 'libclair3'

#295 Thaleslsilva closed 7 months ago
4
Define temporary directory directly from Clair3 CLI

#294 SergeWielhouwer closed 7 months ago
7
Pileup calling fails for downsampled BAMs

#293 fgfrost closed 7 months ago
9
Try to remove the default depth filter in the pileup. Also fix the version

#292 dpryan79 closed 7 months ago
4
Default --qual value?

#291 TristanJang closed 7 months ago
1
ONT R10 Model

#290 HelloYanming closed 7 months ago
1
Calling MNVs

#289 tsneddon closed 7 months ago
4
Ref/Alt number (AD info)

#288 airichli closed 7 months ago
4
Missense variant in FBN2 gene not reported by Clair3

#287 tsneddon closed 7 months ago
4
Fa test

#286 cjw85 closed 7 months ago
3
--qual option not working?

#285 dehui333 closed 7 months ago
2
Intermittent failure during parallel variant calling: Died at /opt/conda/envs/clair3/bin/parallel line 9375, <$fh> chunk 1.

#284 gtollefson closed 7 months ago
1
Failed to Merge gvcf files into multiple gvcf and vcf

#283 Modernism-01 closed 8 months ago
2
Avoid potentially large stack allocation, clean up int usage

#282 cjw85 closed 8 months ago
2
Pileup model to use for full-alignment training step

#281 dehui333 closed 8 months ago
2
Variant is not detected

#280 hillstub closed 7 months ago
1
Is Representation Unification required for all depths for pileup model training?

#279 dehui333 closed 8 months ago
2
pass reference to htsfile for better cram support

#278 ASLeonard closed 8 months ago
2
[ERROR] No pileup model found in provided model path and model prefix

#277 jsromanowski closed 8 months ago
3
Value Error: A BGZF (e.g. a BAM file) block should start with b'\x1f\x8b\x08\x04', not b'\xf12\xdeB'

#276 husamia closed 8 months ago
6
Is there a way to report a MAPQ or MQ metrics?

#275 ghost closed 9 months ago
2
Variant is not detected in amplicon sequencing data

#274 keremozdel closed 8 months ago
4
Unable to install Clair3 with conda issue with tensorflow

#273 sachiwije closed 8 months ago
2
Incorrect SNP representation when it overlaps a deletion

#272 ymcki opened 9 months ago
3
pileup variant for identical genomes

#271 lagphase closed 8 months ago
6
Detect very low SNP frequencies

#270 HJArdin closed 9 months ago
1
genome phasing

#269 DiegoSafian closed 8 months ago
1
Does Clair3 take into account indels proximity when calling SNPs?

#268 ghost closed 9 months ago
2
Conda installation / cant run Clair3

#267 pkerbs closed 8 months ago
1
Why are these SNPs called as RefCall?

#266 weishwu closed 9 months ago
6
Stack overflow seg fault in calculate_clair3_full_alignment

#265 ymcki closed 8 months ago
2
r1041_e82_400bps_hac_v420 model of Guppy basecaller

#264 cuzzlisa closed 9 months ago
3
r1041_e82_400bps_sup_v430 model contains only 4 files

#263 ghost closed 10 months ago
1
Variants below min_coverage still being called

#262 mproberts99 closed 8 months ago
3
Ref calls not printed with `--print_ref_calls` when `--vcf_fn=FILE` is specified

#261 gtollefson closed 8 months ago
9
Send adjacent SNP and Indel candidates both to full-alignment model

#260 haraldgrove opened 10 months ago
9
Do I have to train a model for specific organism?

#259 Modernism-01 closed 10 months ago
4
Snp prediction accuracy is low in all difficult mapping areas

#258 oranges7 closed 11 months ago
1
Variant not detected within 16bp from the start/end

#257 peterk87 opened 11 months ago
11
SNP calling from bisulfite converted ONT

#256 weishwu closed 11 months ago
2
Do I need to filter the input BAMs?

#255 tinyfallen closed 11 months ago
2
Clair3 working over Dorado base caller?

#254 ilivyatan closed 11 months ago
1
Problem with minimum indel AF filter

#253 keremozdel closed 11 months ago
3
parallel: Error:

#252 farhangkl closed 11 months ago
0
Variants called with HiFi but not with ONT in the merge.output.vcf

#251 ghost closed 11 months ago
14
Running Clair on a .bam with mixed flowcell types

#250 fidibidi closed 12 months ago
2
Inaccurate description of the "NON_REF"?

#249 ghost closed 12 months ago
1
model for r10.4.1 cells called with Guppy and not Dorado

#248 ghost closed 11 months ago
12

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