husensofteng
commented
5 years ago it is implemented in the nf pipeline
Closed husensofteng closed 5 years ago
husensofteng
commented
5 years ago it is implemented in the nf pipeline
Translate gnomAD control variants: Input: gene_annotations_gtf: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz genome_fasta: genftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz vep_annotated_vcf: https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz
Input parameters to be set for VCFtoProteinDB.py to process gnomAD VCF file: --transcript_index 6 --annotation_field_name vep --AF_field controls_AF --biotype_str transcript_type