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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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Question regarding reference files #159

Closed teodorabu closed 11 months ago

teodorabu commented 11 months ago

Hi,

I have a question related to the reference files, more exactly what is the difference between the reference files provided in your repository for WES data vs the reference files from the Battenberg repository (for hg19)? I saw in the documentation that it is mentioned how no location filters were applied to the ref WES data derived from the Battenberg files, however the nr of SNPs in the panels varies so I was wondering what filters were applied additionally.

Cheers, Teodora

tlesluyes commented 11 months ago

Hi @teodorabu,

The loci files for hg19 were derived from the 1000 Genomes Project, phase 1 (2012). I'm sure a threshold for AF has been used but I can't say for sure what value was selected. If you need more information, please post your question on the Battenberg GitHub repo.

Cheers,

Tom.