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HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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Detect very low SNP frequencies #270

Closed HJArdin closed 9 months ago

HJArdin commented 9 months ago

Hello, We are looking to test a really low frequencies (2.5, 5, 10, 20%) SNP detection in viral sample. We analyse two BAC with one mutation, mix in different proportion. I use Calir3 with this parameter : -m r1041_e82_400bps_hac_v410/ --haploid_sensitive --include_all_ctgs --snp_min_af=0.01 --min_coverage=10 --no_phasing_for_fa --var_pct_full=1 --ref_pct_full=1 --var_pct_phasing=1 --call_snp_only -p ont

Clair3 catch all SNP > 20% But when the proportion is bellow 20% even if I can see the SNP on IGV image It appears as RefCall in full_alignment.vcf : image And in pileup.vcf: image

Maybe I missunderstand something but why this SNP is tag as a 'RefCall' ?

Best regards, Hugo

aquaskyline commented 9 months ago

Clair3 is for germline mutation, germline mutations have zygosity. For detecting variants with AF<0.2, try ClairS-TO.