1d55b24b30b2f1d69cf1f99f6da7cf5aac40ae40 max Wed Mar 25 07:57:36 2026 -0700 Add database and population config TSV files for varFreqsAll combined track These config files drive the vcfToBigBed.py script that builds the combined variant frequency bigBed. Externalizing the config makes it easy to add new databases or population breakdowns without editing Python code, refs #36642 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/scripts/varFreqs/databases.tsv src/hg/makeDb/scripts/varFreqs/databases.tsv new file mode 100644 index 00000000000..b4885fda40f --- /dev/null +++ src/hg/makeDb/scripts/varFreqs/databases.tsv @@ -0,0 +1,24 @@ +# Database configuration for varFreqsAll combined track +# key name vcf ac_field af_field +# Use "." for fields that don't exist in the VCF +AllOfUs AllOfUs /gbdb/hg38/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz . . +SPARK SPARK WES /gbdb/hg38/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz AC AF +SFARI_WGS SFARI WGS /gbdb/hg38/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz AC AF +GenomeAsia GenomeAsia SNVs /gbdb/hg38/varFreqs/ga100k/ga100k.subst.vcf.gz AC AF +GenomeAsiaIndel GenomeAsia Indels /gbdb/hg38/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz AC AF +KOVA KOVA Korea /gbdb/hg38/varFreqs/kova/kova.v7.vcf.gz AC AF +ToMMo ToMMo Japan /gbdb/hg38/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz AC AF +IndiGen IndiGenomes India /gbdb/hg38/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz AC AF +FinnGen FinnGen Finland /gbdb/hg38/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz AC AF +Saudi Saudi /gbdb/hg38/varFreqs/saudi/saudi.vcf.gz AC AF +SweGen SweGen Sweden /gbdb/hg38/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz AC AF +TOPMed TOPMed /gbdb/hg38/varFreqs/topmed/topmed10.vcf.gz AC AF +ABraOM ABraOM Brazil /gbdb/hg38/varFreqs/abraom/abraom.vcf.gz . AF +ALFA ALFA /gbdb/hg38/varFreqs/alfa/ALFA.vcf.gz . AF_GLB +MGRB MGRB Australia /gbdb/hg38/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz AC AF +HRC HRC /gbdb/hg38/varFreqs/hrc/hrc.vcf.gz AC AF +MexBB Mexico Biobank /gbdb/hg38/varFreqs/mxb/mxb.freq.vcf.gz AC AF +SGDP SGDP /gbdb/hg38/varFreqs/sgdpFreq/sgdp.freq.vcf.gz AC AF +HGDP1kG gnomAD HGDP+1kG /gbdb/hg38/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz AC AF +GREGoR GREGoR /gbdb/hg38/varFreqs/gregor/gregor.vcf.gz AC AF +SCHEMA SCHEMA /gbdb/hg38/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz AC AF