We are excited to announce a collection of new human reference genome sequences that reflect much more global diversity! https://t.co/a39cFG8dOu
— Human Pangenome Reference Consortium (@HumanPangenome) May 10, 2023
My favorite T2T/Pangenome discovery so far: a multi-megabase inverted segmental duplication on the short arm of chr14 that explains the mechanism of Robertsonian translocations. Great writeup by @ScienceStowers "Answering a 50-year-old mystery" https://t.co/u90TGUwnYt pic.twitter.com/wICUL6ISlk
— Adam Phillippy (@aphillippy) May 10, 2023
Brace yourself. The @HumanPangenome tweets are coming! Check out this 🧵 for more details. We're just getting started https://t.co/V8Gu8hdMJX
— Adam Phillippy (@aphillippy) May 10, 2023
dear lazyweb, I used gatk, samtools , delly, manta to discover the SNV and the SV in my bams, to produce multi-samples VCFs
Now, how do I use the new human pangenome reference to perform the same job ?
Approach for germline variant calling is in the linked paper [Applications of the pangenome]. What I get is that giraffe could return a .bam [source] which could be used for downstream analysis. Maybe adding the
vghere on Biostars tag may help getting responses from the vg team.