kemal
c1699b4465
- formats/fasta: plain/BGZF FASTA, .fai/.gzi built identical to htslib, index check, build detection, contig aliases, mmap genome cache (IN-060..064) - formats/bgzf, formats/bcf: pure-Python BGZF, tabix .tbi, BCF 2.2 and CSI (OUT-010, OUT-038, OUT-040) - harmonize/sites: plus-strand mapping with audit rows, indel resolution from SourceSeq (port of GTCtoVCF, Apache-2.0) and left normalisation (OUT-014..021, OUT-030, OUT-042) - harmonize/combine: OUT-031 genotype combination (ploidy-aware, Infinium I/II signal classes, OUT-037) - pipeline/vcf: `simurg gtc-to-vcf` (per-sample VCF.gz+tbi, --merge cohort BCF+csi, audit parquet) - pipeline/export: `simurg export bedgraph|finalreport|plink|locus-summary` (OUT-043, OUT-050..052, OUT-071) - validation: 36 GSA samples vs gtc2vcf: 23.66 M identical calls, 0 unexplained differences; PLINK identical to plink2 on 637,397 variants; bcftools validates VCF/BCF and our indexes answer region queries correctly - fetch_data.sh p6 (Ensembl GRCh38 with checksum), make_oracle_vcf.sh, validate_p6_vcf.py; K-022/K-023
21 lines
1.1 KiB
Bash
Executable File
21 lines
1.1 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Oracle VCFs for phase P6 on the 36 GSA oracle GTCs (needs make_oracle_gtcs.sh and fetch_data.sh p6):
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# * gtc2vcf (MIT) → data/p6/oracle/gsa36_gtc2vcf.vcf.gz (one multi-sample VCF, one record per probe)
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# * optional: GTCtoVCF (Apache-2.0) — python2-era code run under python3 with two local compatibility patches,
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# see docs/validation/P6.md; enable with GTCTOVCF=1.
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set -euo pipefail
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cd "$(dirname "$0")/.."
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B=refs/tools/bcftools-1.22
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export BCFTOOLS_PLUGINS=$B/plugins
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D=data/p0/gsa_v4_pgx
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OUT=data/p6/oracle
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mkdir -p $OUT data/p6/work
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$B/bcftools +gtc2vcf --no-version -t GT,BAF,LRR \
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-b $D/GSA-PGx-48v4-0_20079540_E2_bpm/GSA-PGx-48v4-0_20079540_E2.bpm \
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-c $D/GSA-PGx-48v4-0_20079540_E2_csv/GSA-PGx-48v4-0_20079540_E2.csv \
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-e $D/GSA-PGx-48v4-0_20079540_E2_ClusterFile/GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt \
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-f data/p6/GRCh38.primary.fa -g data/p0/oracle/gsa_gt3_nofma -O u 2> $OUT/gtc2vcf.log \
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| $B/bcftools sort -Oz -o $OUT/gsa36_gtc2vcf.vcf.gz -T data/p6/work/sorttmp
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$B/bcftools index -f -t $OUT/gsa36_gtc2vcf.vcf.gz
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echo "wrote $OUT/gsa36_gtc2vcf.vcf.gz"
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