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Name
Modified
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BAM QC - HG002 (mosdepth coverage + samtools stats)
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16 items
Call HG003 — GATK HaplotypeCaller
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8 items
QC HG002 — bcftools stats + hap.py vs GIAB v4.2.1
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15 items
Call HG004 — GATK HaplotypeCaller
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8 items
Annotate HG002 - VEP (gnomAD AF + SIFT + PolyPhen)
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7 items
Filter HG004 — bcftools norm + GATK hard filters
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4 items
Call HG002 - GATK4 BQSR + HaplotypeCaller
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17 items
Filter HG002 - bcftools normalize + PASS
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4 items
Filter HG003 — bcftools norm + GATK hard filters
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4 items
Uploads
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14 items
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Created
Apr 30, 2026 at 00:45
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Germline SNV + indel calling for a single short-read sample (GIAB HG002, chr20), benchmarked against truth. BAM QC (mosdepth coverage + samtools stats) -> GATK4 BQSR + HaplotypeCaller -> bcftools normalize/filter -> hap.py precision/recall/F1 vs the GIAB v4.2.1 high-confidence set -> VEP functional annotation (gnomAD AF + SIFT + PolyPhen). Reads aligned with BWA-MEM2.
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