Source of chr19 dataset

[nrizzo]

Hello!

I have been reading the experimental section of the PHONI paper and I cannot seem to find the origin of the chromosome 19 dataset. The link in this repo seems no longer active, but the dataset has been used and mirrored here for the PANAMA paper experiments.

Could you share how the dataset was obtained? The FASTA headers contain sample IDs from 1000 genomes project but no other construction info (consensus from called variants? assemblies?). I am not interested in a reproducible pipeline, just the overall methods/sources.

Thank you very much,
Nicola

[maxrossi91]

Hi, Nicola,

The dataset was generated by running bcftools consensus on the msVCF from the 1KGP for each sample's haplotype and concatenated them. Please let me know if you need the full command line and I can dig it up for you.

Bests,

Max

[nrizzo]

Great, thank you! No worries about the full command, I was mainly interested on the type of data present in the sequences (short 1KGP variations). You can close the issue if you want.

Nicola