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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parallel 20191122.* bioconda pin

#347 BioWilko opened 1 day ago
0
Wrong FORMAT specification in VCF file

#346 simondrue closed 1 week ago
2
Warning message is on same line as next error message

#345 mr83-uw closed 1 week ago
0
Difference in number of calls: CRAM vs BAM

#344 nicolechai opened 2 weeks ago
4
Pileup Models for every dorado basecalling model

#343 Rohit-Satyam opened 3 weeks ago
5
The pipeline seems to have stopped with no error

#342 hxlei closed 3 weeks ago
2
Segmentation fault in full_alignment

#341 chris-cheshire closed 1 week ago
6
Variant calling in mito: No vcf file found, output empty vcf file

#340 juanjo255 closed 1 month ago
7
Which model should I use for R9.4.1 data basecalled with dorado

#339 eesiribloom closed 3 weeks ago
1
Mito variant calling

#338 leonschuetz closed 1 month ago
1
Updated models

#337 assafgrw closed 1 month ago
1
malformed metadata and header in temporary vcfs when running clair3 with whatshap phase with large bam file

#336 blackbeerd closed 1 month ago
2
Not detecting variants below 10% and incorrect allele frequencies

#335 daysmcgrath closed 1 month ago
0
Missing calls with --min_coverage=1

#334 gc-content closed 2 months ago
2
No vcf output from clair3 run

#333 lynnjo closed 3 months ago
3
Very slow processing of low-quality chrX variants with full-alignment model

#332 esraaelmligy closed 2 months ago
3
Clair3 with polyploids

#331 ewoutcrombez closed 2 months ago
1
Broken pipe error

#330 osvatic closed 2 months ago
2
Using HERRO corrected reads in Clair3

#329 KANGYUlab closed 2 months ago
2
erro corrected reads

#328 KANGYUlab closed 3 months ago
0
minor bug with conda install `import: command not found`

#327 gbouras13 closed 1 week ago
2
REF=TGTGB

#326 minw2828 closed 3 months ago
4
Exit in environment checking

#325 xiaolongliang closed 3 months ago
2
descriptions of outputs available?

#324 osvatic closed 3 months ago
0
Which model?

#323 ascialla closed 3 months ago
1
Clair3 with T2T aligned reads

#322 DHmeduni closed 3 months ago
1
upgrading longphase to 1.7.3

#321 signalbox2 closed 3 months ago
2
show more allele counts in INFO

#320 hoyonh opened 4 months ago
3
[ERROR] Model path not found

#319 Wshengquan closed 4 months ago
4
choose pileup call over full-alignment call if pileup call has 1) a way higher QUAL, 2) is an indel

#318 drtconway opened 4 months ago
3
Clair3 GVCF created file is 1bp of the end sequence so validatevariants fails

#317 JosephThorpe closed 3 months ago
4
Correct variant found by pileup is changed after full alignment

#316 f-ferraro closed 4 months ago
1
Unexpected 0/0 records

#315 Krannich479 closed 4 months ago
2
Run does not respect AF settings

#314 Krannich479 closed 5 months ago
2
Clair3 docker numpy compatibility

#313 DNA-Dave closed 4 months ago
2
It took 10 hrs to call variants against ~40MB reads via Docker Clair3

#312 RunpengLuo closed 5 months ago
2
Error merging GVCFs of multiple samples in cDNA sequencing experiment

#311 eiwai81 closed 5 months ago
8
Using a bam file with haplotag information with Clair3

#310 eaooms closed 4 months ago
6
HG003 pacbio CCS hifi data cannot get

#309 shiying-sxu closed 4 months ago
0
Optimize pileup calling for high throughput targeted amplicon bed files

#308 Permafacture closed 4 months ago
1
Link to fa file is broken

#307 v-lakhujani closed 5 months ago
3
Inefficient in high-throughput, targeted amplicon use case

#306 Permafacture closed 4 months ago
4
Read Depth in VCF

#305 mproberts99 closed 5 months ago
4
print_version reports wrong version in 1.0.8

#304 SamStudio8 closed 5 months ago
1
The same input bam, fasta and models, but different output size of merge_output.vcf.gz

#303 Jerry-is-a-mouse closed 5 months ago
5
Best practices to use different and/or new models for variant calling

#302 EmilioKolo closed 6 months ago
2
Split chromosomes for calling variant like gatk.

#301 RADIOMUMM closed 7 months ago
1
training model

#300 Mona3130 closed 6 months ago
2
Issues with Variant Detection in ONT Dataset Using Clair3

#299 DaliBAmor closed 6 months ago
0
No contig intersection found, output header only in /lab/user/data/test1/clair3/merge_output.vcf.gz

#298 DaliBAmor closed 7 months ago
4