How to use Minigraph-cactus pan genome to poplualtion analysis

[ld9866]

Dear developer: At present, we have built a graphical pan-genome using 27 genomes, and then we want to map a batch of population data into our pan-genome, which is very easy to obtain vcf variation information of individuals after obtaining gam files through vg Giraffe and converting them. I wonder if we can directly use bcftools for post-merge analysis as easily as GATK.

Besides, we want to do population level analysis only for SV greater than 50BP, how do I do this? Best

[glennhickey]

You should be able to use bcftools to merge. It helps if you run vg call with -a if you're using vg call. You can use bcftools norm -f to left shift your variants which may help, and truvari has some functionality for merging SVs as well.

[ld9866]

Dear developer: We want to translate the MC result (vcf) to biallelic type because we want to use the PanGenie to genotype our population, l want to ask how to do this step? Best