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1000 Genomes related SV calls #8

Open samkleeman1 opened 2 years ago

samkleeman1 commented 2 years ago

Hi,

Many thanks for making all code and data available. I am very keen to access this file (https://cgl.gi.ucsc.edu/data/giraffe/products/vggiraffe-sv-relkgp-raw.vcf.gz) reflecting the SV calls from the related subjects in 1000 Genomes. Currently this file is identical to the file containing unrelated subjects (https://cgl.gi.ucsc.edu/data/giraffe/products/vggiraffe-sv-2504kgp-raw.vcf.gz) and so this data is not available. I would be incredibly grateful if you can share this data with us.

Kind regards,

Dr Sam Kleeman MD PhD Student Cold Spring Harbor Laboratory, NY

adamnovak commented 2 years ago

Our apologizes; we do appear to have stored the unrelated samples Giraffe SV VCF again, instead of the one for the related samples. This is how it was in our IPFS data archive in the submission, and in our scratch S3 bucket.

We're looking into whether we can pull the calls for those samples out of the Terra runs, or whether they have been deleted and the WDLs would need to be re-run.

The writeup for what we did here is https://github.com/vgteam/giraffe-sv-paper/tree/0e81331b6d4ae27461c7d8b907ef33dad6fddc46/scripts/sv/genotype-svs#sv-genotyping-on-terra, but it doesn't seem to cover exactly how we did the step where we pulled the individual VCFs from Terra and merged them, which is presumably where things went wrong.

adamnovak commented 2 years ago

@jmonlong I think you went looking for this, right? Did we ever find the calls for the related people?