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• make_beagle_chunks improvement

Dear Team,

Is there any plan/roadmap to re-alignment and call the variants with T2T-CHM13?

Thanks.

Shicheng

For the IGSR/1000 genomes project downloaded from EBI at this location:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/

We are concerned it what looks like a truncated file for ChrX in this list. It has considerably smaller size than any of the other per-chr VCF files and after running it through conversations and plots ourselves, the last variant in the file is only at ChrX: 2,781,455.

Since UCSC picked up these VCF files as input to their track, you can even see where the chrX variants stop in their genome browser:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chrX%3A2715741%2D2855483&hgsid=1039559061_PwN1CAfq0fa6MajfjbgjE7OAT3Xe

If you know who we may contact that may have the full un-truncated chrX of this source, we would appreciate it.

It looks like this chromosome needs to be recalled, and UCSC may need to notified to update their source data as well.