Clair3

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pass reference to htsfile for better cram support

1

Although cram files are supported, I believe it only works if you have internet connection to download or a local cache of the reference genome. Without these you get decode...

ASLeonard

pileup variant for identical genomes

3

Hi, I have high quality ONT reads from a single cell that passed all the quality check. I assembled these reads into a genome, then used Clair3 on the reads...

lagphase

Unable to install Clair3 with conda issue with tensorflow

2

Hi, I am getting the following issue when trying to install clair3 using conda. Thanks. ``` (base) ➜ ~ conda create -n clair3 -c bioconda clair3 python=3.9.0 -y Channels: -...

sachiwije

Incorrect SNP representation when it overlaps a deletion

3

When I was trying to run vcfeval with the same vcf generated by Clair3 using the following command, I find that I am getting 3518 out of 5440881 FPs/FNs ./rtg...

ymcki

Hello, I just tried the Installation from Bioconda like this: ``` mamba create -n clair3_env -c bioconda clair3 mamba activate clair3_env ``` Unfortunately, there is no `clair.sh` in my environment...

pkerbs

Variants below min_coverage still being called

2

Hi, I have set the min_coverage parameter to 10, but am still observing calls with read counts below that number in the final VCF. When I up the parameter to...

mproberts99

Ref calls not printed with `--print_ref_calls` when `--vcf_fn=FILE` is specified

8

Hi, When I run the following clair3 command with --vcf_fn and --print_ref_calls provided, reference records report the genotype as ./. and don't report the other format fields (DP, etc.) ```...

gtollefson

Stack overflow seg fault in calculate_clair3_full_alignment

1

I ran a high coverage sample and got seg fault with clair3.py CallVariantsFromCffi running 1.0.4 Running a version of python3.9-debug allowed me to pinpoint the crash at clair3_full_alignment.c:656 which is...

ymcki

Send adjacent SNP and Indel candidates both to full-alignment model

9

I've been running Clair3 (v1.01) on some pig samples with ONT reads. I noticed that Clair3 has been assigning the "1/1" genotype to SNVs that have an allele frequency where...

haraldgrove

Error while opening BGZF compressed FASTA reference file

2

Running clair3 without `--longphase_for_phasing` results in an error when using a bgzipped reference indexed with samtools: ```bash apptainer exec clair3-v0.1-r12.sif \ /opt/bin/run_clair3.sh \ --bam_fn=test.cram \ --ref_fn=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \ --platform="ilmn" \ --model_path="/opt/models/ilmn"...

dennishendriksen