Collects commonly used capture region BED files. These are installed and available for use in bcbio analyses. Includes files for hg19 (chr1, chr2, chr3... style naming) and GRCh37 (1, 2, 3... style naming).
capture_regions/Exome-AZ_V2-- Inclusive file of exome regions, hand curated by AstraZeneca Oncology.capture_regions/Exome-IDT_V1-- IDT xGen Exome Research Panel v1.0capture_regions/Exome-Agilent_V6-- Agilent SureSelect Human All Exon V6capture_regions/Exome-Agilent_V5_Clinical-- Agilent SureSelect Clinical Research Exomecapture_regions/Exome-MedExome-- Nimblegen SeqCap EZ MedExomecapture_regions/Exome-NGv3-- Nimblegen SeqCap EZ Exome v3
Files under transcripts/cancer_transcripts_*_ensembl.txt contain IDs of canonical (longest) transcripts that are used by SnpEff variant prediction tool when it run with the -canon flag (only in Ensembl-based versions of reference databases GRCh37.** and GRCh38.** in SnpEff notation). Since not all IDs in the list represent the most cancer-relevant isoforms, transcripts/canon_cancer_replacement.txt provides a map of transcripts for replacement with the -canonList option:
java -jar snpEff.jar GRCh37.75 test.vcf -canon -canonList transcripts/canon_cancer_replacement.txt
To use the canonical transcripts for variant annotation in bcbio, add the following into your configuration YAML file:
algorithm:
effects_transcripts: canon
To use the cancer transcripts, use the following:
algorithm:
effects_transcripts: canonical_cancer
The full list of genes with replaced transcripts:
AKT1 ENST00000555528
BRCA1 ENST00000357654
CD79B ENST00000006750
CDKN2A ENST00000304494
CHEK1 ENST00000534070
CHEK2 ENST00000328354
ESR1 ENST00000206249
FANCL ENST00000233741
FGFR1 ENST00000447712
FGFR2 ENST00000457416
FGFR3 ENST00000440486
MET ENST00000397752
MYD88 ENST00000396334
PPP2R2A ENST00000380737
RAD51D ENST00000345365
RAD54L ENST00000371975
GNAS ENST00000371085
TP53 ENST00000269305
ARID1B ENST00000350026
TET2 ENST00000380013
CEBPA ENST00000498907
PIK3C2G ENST00000538779