search

gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
138 stars 45 forks source link

rnaVariantCalling high-quality SNPs for hg38 in documentation #578

Open yunkaig opened 2 months ago

yunkaig commented 2 months ago

Hi there,

I am downloaded input files according to the documentation here: https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#files-to-download

For the high-quality variants, I can see there is one file for SNPs and one for INDELs for hg19, but for hg38 both files are for INDELs. Is there are particular reason for that?

Many thanks, Yunkai

vyepez88 commented 2 months ago

Hi Yunkai, for hg38, the files are downloadable here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

yunkaig commented 2 months ago

Hi @vyepez88,

Sorry I might not have been clear. I saw this on the documentation page:

image

For hg19 there is one file for indel and another for snp.

But for hg38 both files are for indels.

Is that how it is supposed to be?

Many thanks!