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Resource creation

Gene annotations

First download APPRIS annotations so that we can select the most relevant transcripts.

base_url=https://apprisws.bioinfo.cnio.es/pub/releases/2023_08.v48/datafiles/homo_sapiens

wget -O resources/appris.e105v46.tsv ${base_url}/e105v46/appris_data.appris.txt
wget -O resources/appris.rs110v48.tsv ${base_url}/rs110v48/appris_data.appris.txt

Annotations from Ensembl 105, HGNC, and RefSeq are used to reference genes in a consistent way, enabling exact and confident comparison between different sources. The Ensembl 105 annotations are obtained from the GENCODE v39 release and processed to be readily usable.

wget -P resources/ https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz

./scripts/compile_annotation_data.py \
  ensembl \
  --annotations_fp resources/gencode.v39.annotation.gtf.gz \
  --appris_fp resources/appris.e105v46.tsv \
  --output_dir ./resources/

As some genes are not present in Ensembl 105 (e.g. IGH, TRA), I use RefSeq v110 annotation release inplace of Ensembl when necessary. As RefSeq annotations use accessions for contigs, these must be renamed with using a lookup table.

base_ftp=https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_000001405.40_GRCh38.p14
wget -P resources/ ${base_ftp}/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz

curl ${base_ftp}/GCF_000001405.40_GRCh38.p14_assembly_report.txt | \
  awk 'BEGIN { OFS="\t" } $0 ~ /^MT|^[0-9XY]/ { print "chr" $1, $7 }' | \
  sed 's/chrMT/chrM/' > resources/refseq_contig_id_mapping.tsv

./scripts/compile_annotation_data.py \
  refseq \
  --annotations_fp resources/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz \
  --appris_fp resources/appris.rs110v48.tsv \
  --contig_mapping_fp resources/refseq_contig_id_mapping.tsv \
  --output_dir ./resources/

I've anecdotally observed that source gene symbols match at a higher rate to the latest HGNC database release compared to the release tied with Ensembl 105. The general process taken is to match gene symbols against the latest HGNC database release and subsequently add the Ensembl 105 gene annotations. Hence, we retrive the latest HGNC complete set.

wget -P resources/ https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/hgnc_complete_set_2023-11-01.tsv

Hartwig Ensembl data cache and Gene Utilities

We use hmftools workflows/components from Hartwig in our post-processing pipelines, and this requires specific data files to be generated from the UMCCR gene panels. These data files are created with gene-utils for the somatic panel and fusion panel. Beyond the panel data files, we must also build the hmftools Ensembl data cache for both the hmftools workflows and certain gene-utils functions.

First compile gene-utils at commit a156ed6 (current v1.0 release is missing important changes), see COMPILE_GENE_UTILS.md.

Build the Ensembl data cache for GRCh38 from the Ensembl 105 release

mkdir -p resources/hmftools_ensembl_data_cache/

java \
  -cp other/gene-utils_a156ed6.jar \
  com.hartwig.hmftools.geneutils.ensembl.GenerateEnsemblDataCache \
    -ensembl_user anonymous \
    -ensembl_db mysql://ensembldb.ensembl.org:3306/homo_sapiens_core_105_38 \
    -ref_genome_version 38 \
    -log_debug \
    -output_dir resources/hmftools_ensembl_data_cache/