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HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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SNP missing #240

Closed HJArdin closed 1 year ago

HJArdin commented 1 year ago

Hello, I'm testing Clair3 to identify drugs resistance mutation and some snp are not found even if they are in .bam file and can be see on IGV. image image Other snp with less coverage/frequence are detect. Here is the command I used : 

run_clair3.sh -b 50E150E2_MixA1.trimmed.rg.sorted.bam -f ./primer-schemes/custom_CMV/V8/custom_CMV.reference.fasta -m clair3_models/r941_prom_hac_g360+g422/ --include_all_ctgs -t 25 --snp_min_af=0.1 --indel_min_af=0.15 --haploid_sensitive -p ont -o .

Some idea why I can't find this two snp ?

aquaskyline commented 1 year ago

If you are dealing with amplicon data, please try setting --var_pct_full, --ref_pct_full and --var_pct_phasing to 1.

HJArdin commented 1 year ago

Thanks you, it looks like it works for the second one but the first is still not in VCF

Edit: nvm all works fine thanks you !