SNP missing

[HJArdin]

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.


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]

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

[HJArdin]

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 !