kemal
a8caa26aa4
- qc/controls: canonical control names (QC-002), bkg/offset (QC-003), 13 genotyping metrics (QC-004/005), missing/zero-divisor handling (QC-007/008); controls_raw.tsv / controls_qc.tsv (QC-009/011) incl. compat CSVs - qc/thresholds + profiles: YAML schema, validation codes, precedence, shipped profiles, auto (QC-020..025) - qc/status: functional PASS/FAIL/NA, control CLEAR/FLAGGED, flags (QC-030..033) - qc/contamination: BAF regression; bit-compatible with gtc2vcf BAFregress (36/36, K-017), exact mode too - qc/relatedness: KING-robust, duplicates, Mendelian errors, pedigree from sheet (IN-018) - qc/locus_summary: OUT-072, bit-identical to BeadArrayFiles except ChiTest (K-018) - qc/suggest: suggest-thresholds (QC-026) - pipeline/qc: disk-backed cohort store; CLI qc controls|samples|contamination|relatedness|loci|suggest-thresholds - genotype: control tables (OUT-070), het_rate, QC columns, cohort QC - tests: unit + oracle (BAFregress plugin, BeadArrayFiles locus summary)
39 lines
2.0 KiB
Bash
Executable File
39 lines
2.0 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Build bcftools + gtc2vcf plugins (MIT) under refs/tools and generate oracle GTC files from the P0 GSA demo IDATs,
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# once per normalization version (GenTrain 3 = normalization 1.2.0, GenTrain 2 = 1.1.2).
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# The plugin is compiled with -ffp-contract=off: compilers may otherwise fuse a*b+c into FMA instructions (default
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# on aarch64), which changes the last bits of the normalization transforms. Vendor .NET code and NumPy do not fuse.
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# Usage: bash scripts/make_oracle_gtcs.sh [chip-folder ...] (default: every chip in the demo set)
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set -euo pipefail
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cd "$(dirname "$0")/.."
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V=1.22
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T=refs/tools
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B=$T/bcftools-$V
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if [[ ! -x $B/bcftools || ! -f $B/plugins/idat2gtc.so || ! -f $B/plugins/BAFregress.so ]]; then
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[[ -d refs/gtc2vcf ]] || bash scripts/bootstrap_refs.sh
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mkdir -p $T
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[[ -f $T/bcftools.tar.bz2 ]] || curl -sL -o $T/bcftools.tar.bz2 \
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"https://github.com/samtools/bcftools/releases/download/$V/bcftools-$V.tar.bz2"
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tar -xjf $T/bcftools.tar.bz2 -C $T
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rm -f $B/plugins/{idat2gtc,gtc2vcf,affy2vcf,BAFregress}.{c,h}
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cp refs/gtc2vcf/{idat2gtc,gtc2vcf,affy2vcf,BAFregress}.c refs/gtc2vcf/*.h $B/plugins/
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(cd $B/htslib-$V && ./configure --disable-libcurl --disable-bz2 --disable-lzma --disable-ref-cache >/dev/null)
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(cd $B && ./configure --without-gsl >/dev/null && make -j"$(nproc)" CFLAGS="-g -O2 -ffp-contract=off" >/dev/null)
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fi
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export BCFTOOLS_PLUGINS=$B/plugins
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D=data/p0/gsa_v4_pgx
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IDATS=$D/idats_Demo_36/idats_Demo_36
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chips=("$@")
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[[ ${#chips[@]} -eq 0 ]] && mapfile -t chips < <(find "$IDATS" -mindepth 1 -maxdepth 1 -type d | sort)
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for v in 3 2; do
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OUT=data/p0/oracle/gsa_gt${v}_nofma
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mkdir -p "$OUT"
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for chip in "${chips[@]}"; do
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$B/bcftools +idat2gtc --gentrain-version $v \
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--bpm $D/GSA-PGx-48v4-0_20079540_E2_bpm/GSA-PGx-48v4-0_20079540_E2.bpm \
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--egt $D/GSA-PGx-48v4-0_20079540_E2_ClusterFile/GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt \
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--idats "$chip" --output "$OUT" 2>&1 | grep -E "^(Call rate|Gender|Writing)" || true
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done
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echo "oracle GTCs in $OUT: $(ls "$OUT"/*.gtc | wc -l)"
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done
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