Dan Bolser

Thanks for looking at this Liubov. Are you actively using ATAC?

To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based database data.

Hi Liguo, Thanks for getting back to me . The chain file I'm using is here: ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz Our internal (1-based) database has the following mapping: V2: 64231291 to 64603896 -> V3: 71417888 to 71790493 When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputting this works: 1 64231291 64603896 but if I 'properly' 0-base the bed file:...

To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based data.

Hi Liguo, Thanks for getting back to me . The chain file I'm using is here: ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz Our internal (1-based) database has the following mapping: V2: 64231291 to 64603896 -> V3: 71417888 to 71790493 When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputtign this works: 1 64231291 64603896 but if I 'properly' 0-base the bed file:...

BED off by one projection error.

Mapping VCF over an inversion doesn't revcomp the alleles

matchExtender: Assertion `0' failed