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HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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Variant is not detected #280

Closed hillstub closed 7 months ago

hillstub commented 8 months ago

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=<ID=PASS,Description="All filters passed">
##FILTER=<ID=LowQual,Description="Low quality variant">
##FILTER=<ID=RefCall,Description="Reference call">
##INFO=<ID=P,Number=0,Type=Flag,Description="Result from pileup calling">
##INFO=<ID=F,Number=0,Type=Flag,Description="Result from full-alignment calling">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ<20 or selected by 'samtools view -F 2316' are filtered)">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Observed allele frequency in reads, for each ALT allele, in the same order as listed, or the REF allele for a RefCall">
##contig=<ID=077fe5c3b2134307b51035f0,length=1607>
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  SAMPLE
077fe5c3b2134307b51035f0    864 .   G   A   10.01   PASS    P   GT:GQ:DP:AD:AF  0/1:10:301:64,228:0.7575
077fe5c3b2134307b51035f0    974 .   C   A   14.29   PASS    P   GT:GQ:DP:AD:AF  1/1:14:301:55,232:0.7708
077fe5c3b2134307b51035f0    978 .   A   G   10.45   PASS    P   GT:GQ:DP:AD:AF  1/1:10:301:68,225:0.7475
077fe5c3b2134307b51035f0    980 .   C   G   11.42   PASS    P   GT:GQ:DP:AD:AF  1/1:11:301:60,224:0.7442
077fe5c3b2134307b51035f0    985 .   C   A   7.79    PASS    F   GT:GQ:DP:AD:AF  1/1:7:301:64,224:0.7442

But IGV shows a snp at 984:

image
zhengzhenxian commented 8 months ago

@hillstub Could you pls check if the site 984 was found in the pileup.vcf.gz?