Clair3
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HKU-BAL
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Hello , I use clair3 on my Nanopore data. I have a question about the Depth. I determine the overall depth of my bam file with MosDepth (https://github.com/brentp/mosdepth). And when...
The default installation environment for Clair3 uses Python 3.6.10 (https://github.com/HKU-BAL/Clair3/blob/main/Dockerfile#L25). Python 3.6 has reached end of life and has not received security updates since December 2021. Unless there are specific...
Hello, I am unsure of the model I should use for Minion r9.4.1 where the base calling was performed with dna_r9.4.1_450bps_fast.cfg I saw a "fast" compatible model for r10.4 from...
Clair3 packages [longphase 1.0](https://github.com/HKU-BAL/Clair3/blob/main/Makefile#L10), but we have been unable to use CRAM input with longphase < 1.3 due to a defect that was fixed [by this commit](https://github.com/twolinin/longphase/commit/5d450a3b7900271974a1610e73809cc3f12a60db). This requires us...
Hello, I am using clair3 for variant calling on Nanopore data (running with default parameters, excpt for --include_all_ctgs). I observed, that clair3 seems to not call possible variants within up...
I'm starting to investigate various memory errors we have seen with clair3 code. This commit is a small one have getting acquianted with the bits full alignment feature code (the...
For some reason, it's missing variants. This is the merge vcf: ``` ##fileformat=VCFv4.2 ##source=Clair3 ##clair3_version=1.0.4 ##cmdline=/opt/bin/run_clair3.sh --bam_fn=/root/clair3/input/A10.bam --ref_fn=/root/clair3/input/reference.fasta --threads=2 --platform=ont --model_path=/opt/models/r1041_e82_400bps_sup_v420 --output=/root/clair3/output --include_all_ctgs --snp_min_af=0.01 --qual=1 --no_phasing_for_fa ##reference=/root/clair3/input/reference.fasta ##FILTER= ##FILTER= ##FILTER=...
Hello, I noticed that Clair3 is not calling a variant near the end of a short reference sequence (position 2265 of Influenza A virus PB2 sequence [OP597571.1](https://www.ncbi.nlm.nih.gov/nuccore/OP597571.1); sequence length=2280). Bcftools...
Value Error: A BGZF (e.g. a BAM file) block should start with b'\x1f\x8b\x08\x04', not b'\xf12\xdeB'
command using docker `docker run --rm -it -v /mnt/e/E:/EEE hkubal/clair3:latest bash` `/opt/bin/run_clair3.sh --bam_fn=/data/41195.minimap2.bam --ref_fn=/data/Homo_sapiens_assembly38.fasta.gz --output=/data/Clair3_41195 --remove_intermediate_dir --enable_long_indel --threads=40 --platform=ont --model_path=/opt/models/r941_prom_sup_g5014 --sample_name=41195 ` Error ``` # Working on contig chr2 in...
Hi, I am writing because I want to phase a genome that I assembled using nanopore long reads and then I used HiC data to scaffold chromosomes. I was wondering...
