Clarification on Genotyping Mode in CLAIRS-TO

[rcools]

Hey developers,

In my study, I'm only interested in calling variants at specific loci. For this reason, I used the genotyping mode of CLAIRS-TO (specified with the -G flag). However, I couldn’t find a clear explanation of what this genotyping mode entails. Does it require less input data or context compared to the regular variant calling mode? Also, is there a difference in behavior when providing a BED file without enabling genotyping mode?

Thanks in advance for your help!

[JasonCLEI]

Hi @rcools ,

To achieve your goal of calling variants at specific loci, ebabling the genotyping mode by adding the option -G VCF_FN or --genotyping_mode_vcf_fn VCF_FN, or specifying the BED file by adding the option -b BED_FN or --bed_fn BED_FN, are both feasible solutions. If you are using the genotyping mode, you should provide a VCF file containing the candidate sites of your interest to be called. Compared to directly specifying the BED file, ebabling the genotyping mode will force the model to call the specific loci as long as there are supporting reads at this site and relax some VAF and supporting reads constraints.

Lei