"annotate_gnomad_v2_variants_with_mnvs",
annotate_variants_with_mnvs,
"/gnomad_v2/gnomad_v2_variants_annotated_1.ht",
{
"variants_path": pipeline.get_task("prepare_gnomad_v2_variants"),
"mnvs_path": pipeline.get_task("prepare_gnomad_v2_mnvs"),
},
)
pipeline.add_task(
"annotate_gnomad_v2_transcript_consequences",
annotate_transcript_consequences,
"/gnomad_v2/gnomad_v2_variants_annotated_2.ht",
{
"variants_path": pipeline.get_task("annotate_gnomad_v2_variants_with_mnvs"),
"transcripts_path": genes_pipeline.get_task("extract_grch37_transcripts"),
},
)
###############################################
# LoF curation
###############################################
pipeline.add_task(
"prepare_gnomad_v2_lof_curation_results",
import_gnomad_v2_lof_curation_results,
"/gnomad_v2/gnomad_v2_lof_curation_results.ht",
{"genes_path": genes_pipeline.get_task("prepare_grch37_genes")},
{
"curation_result_paths": [
"gs://gnomad-public/truth-sets/source/lof-curation/AP4_curation_results.csv",
import_exac_vcf,
"/exac/exac_variants.ht",
{
"path":
"gs://gnomad-public/legacy/exac_browser/ExAC.r1.sites.vep.vcf.gz"
},
)
pipeline.add_task(
"annotate_exac_transcript_consequences",
annotate_transcript_consequences,
"/exac/exac_variants_annotated_1.ht",
{
"variants_path": pipeline.get_task("import_exac_vcf"),
"transcripts_path":
genes_pipeline.get_task("extract_grch37_transcripts"),
},
)
###############################################
# Coverage
###############################################
pipeline.add_task(
"import_exac_coverage",
import_exac_coverage,
"/exac/exac_coverage.ht",
)
###############################################
# Run
def truncate_clinvar_variant_ids(ds):
return ds.annotate(variant_id=hl.if_else(
hl.len(ds.variant_id) >= 32_766, ds.variant_id[:32_632] +
"...", ds.variant_id))
DATASETS_CONFIG = {
##############################################################################################################
# Genes
##############################################################################################################
"genes_grch37": {
"get_table":
lambda: hl.read_table(
genes_pipeline.get_task("annotate_grch37_genes_step_3").
get_output_path()),
"args": {
"index":
"genes_grch37",
"index_fields": [
"gene_id", "symbol_upper_case", "search_terms", "xstart",
"xstop"
],
"id_field":
"gene_id",
"block_size":
200,
},
},
"genes_grch38": {
"get_table":
"download_clinvar_grch38_vcf",
"ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz",
"/external_sources/clinvar_grch38.vcf.gz",
)
pipeline.add_task(
"prepare_clinvar_grch38_variants",
prepare_clinvar_variants,
"/clinvar/clinvar_grch38_base.ht",
{"vcf_path": pipeline.get_task("download_clinvar_grch38_vcf")},
{"reference_genome": "GRCh38"},
)
pipeline.add_task(
"annotate_clinvar_grch38_transcript_consequences",
annotate_transcript_consequences,
"/clinvar/clinvar_grch38_annotated.ht",
{
"variants_path": pipeline.get_task("prepare_clinvar_grch38_variants"),
"transcripts_path": genes_pipeline.get_task("extract_grch38_transcripts"),
"mane_transcripts_path": genes_pipeline.get_task("import_mane_select_transcripts"),
},
)
###############################################
# Run
###############################################
if __name__ == "__main__":
run_pipeline(pipeline)