a5c699a7301156154700f51a20ae571bc6987051
max
  Sat Sep 26 17:53:41 2026 -0700
varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424

diff --git src/hg/makeDb/scripts/varFreqs/sparkWgs45kToVcf.sh src/hg/makeDb/scripts/varFreqs/sparkWgs45kToVcf.sh
deleted file mode 100644
index 729785431d0..00000000000
--- src/hg/makeDb/scripts/varFreqs/sparkWgs45kToVcf.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/bin/bash
-# Build the SFARI SPARK WGS 45k sites VCF from the release's AF table.
-# Usage: sparkWgs45kToVcf.sh <pvcf_variant_frequencies.tsv> <out.vcf.gz> [threads]
-# Splits the table per chromosome, converts each with sparkWgs45kToVcf.py
-# (AN estimate, AC=round(AF*AN), singletons dropped), left-aligns with
-# bcftools norm, sorts and concatenates into one bgzipped, tabix-indexed VCF.
-set -euo pipefail
-
-inTsv=$1
-outVcf=$2
-threads=${3:-24}
-scriptDir=$(dirname "$(readlink -f "$0")")
-refFa=/hive/data/genomes/hg38/bed/varFreqs/all/hg38.fa
-work=$(dirname "$outVcf")/work
-mkdir -p "$work"
-
-# 1. split by chromosome in one pass (input is already sorted by chrom)
-awk -F'\t' -v d="$work" 'NR>1 {if ($1!=c) {if (f) close(f); c=$1; f=d"/"c".tsv"} print > f}' "$inTsv"
-
-# 2. convert + left-align/trim + sort, per chromosome in parallel
-python3 "$scriptDir/sparkWgs45kToVcf.py" -H /dev/null > "$work/header.vcf" 2>/dev/null
-convertOne() {
-    c=$1; work=$2; scriptDir=$3; refFa=$4
-    (cat "$work/header.vcf"; python3 "$scriptDir/sparkWgs45kToVcf.py" "$work/$c.tsv" 2> "$work/$c.convert.log") \
-      | bcftools norm --check-ref w -f "$refFa" -Ou 2> "$work/$c.norm.log" \
-      | bcftools sort -T "$work/sort.$c" -m 4G -Ob -o "$work/$c.bcf"
-    bcftools index "$work/$c.bcf"
-}
-export -f convertOne
-ls "$work"/chr*.tsv | xargs -n1 basename | sed 's/.tsv$//' \
-    | parallel -j "$threads" convertOne {} "$work" "$scriptDir" "$refFa"
-
-# 3. concatenate in chrom.sizes order
-chroms=$(cut -f1 /hive/data/genomes/hg38/chrom.sizes | grep -v _ | sort -V)
-files=""
-for c in $chroms; do [ -s "$work/$c.bcf" ] && files="$files $work/$c.bcf"; done
-bcftools concat --threads 8 -Oz -o "$outVcf" $files
-tabix -p vcf "$outVcf"
-
-cat "$work"/chr*.convert.log
-grep -h 'Lines' "$work"/chr*.norm.log || true