Clarification on Reference Version in GATK Resource Bundle

Question

[George]

Hey everyone,

I'm currently working with GATK and following the best practices, specifically using the hg38 reference from their resource bundle. However, I'm trying to find an annotation file (GFF or GTF) that matches this reference, and I'm not sure about the exact .p version GATK uses in its resource bundle.

Does anyone know the specific .p version for the hg38 reference in the GATK resource bundle? Unfortunately, they don't provide an annotation file, so knowing the exact reference version would be really helpful.

Here's the link to the resource bundle for reference: Google Cloud Storage - GATK Resource Bundle

Thanks in advance for your help!

Answer 1

[GenoMax]

Resource bundle uses the following files. It tells us they are using GENCODE release v.27.

Reference name  Location
genome_ref_fasta    gs://gcp-public-data--broad-references/hg38/v0/GRCh38.primary_assembly.genome.fa
rrna_intervals  gs://gcp-public-data--broad-references/hg38/v0/gencode.v27.primary_assembly.annotation.interval_list
gene_ref_flat   gs://gcp-public-data--broad-references/hg38/v0/GRCh38_gencode.v27.refFlat.txt
hisat2_ref_index    gs://gcp-public-data--broad-references/hg38/v0/hisat2_primary_gencode_human_v27.tar.gz
hisat2_ref_trans_index  gs://gcp-public-data--broad-references/hg38/v0/hisat2_from_rsem_star_primary_gencode_human_v27.tar.gz
rsem_ref_index  gs://gcp-public-data--broad-references/hg38/v0/rsem_primary_gencode_human_v27.tar

GENCODE_v27 can be found here: https://www.gencodegenes.org/human/release_27.html

[George]

ty, you are great :) \ Sorry if the question was a waste of time