kemal
8758178df6
Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking (MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006, bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878).
99 lines
2.9 KiB
YAML
99 lines
2.9 KiB
YAML
# Canonical control-probe IDs (spec QC-002). Keys are *normalised* names: case-folded, whitespace collapsed,
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# no spaces next to or inside parentheses, "bgnd" written as "bkg". Several manifest spellings map to one ID.
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canonical:
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# staining
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biotin(high): biotin_high
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biotin(bkg): biotin_bkg
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biotin(5k): biotin_5k
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dnp(high): dnp_high
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dnp(bkg): dnp_bkg
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dnp(20k): dnp_20k
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# extension
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extension(a): ext_A
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extension(t): ext_T
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extension(c): ext_C
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extension(g): ext_G
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# hybridization
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hyb(high): hyb_high
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hyb(medium): hyb_medium
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hyb(low): hyb_low
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# target removal
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target removal: target_removal_1
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target removal(1): target_removal_1
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target removal 1: target_removal_1
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target removal(2): target_removal_2
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target removal 2: target_removal_2
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# stringency
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string(pm): string_pm
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string(mm): string_mm
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# non-specific binding (one bead type per colour label on genotyping chips)
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nsb(bkg): nsb_bkg
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nsb(bkg) red: nsb_bkg
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nsb(bkg) green: nsb_bkg
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nsb(bkg) blue: nsb_bkg
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nsb(bkg) purple: nsb_bkg
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# non-polymorphic
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np(a): np_A
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np(t): np_T
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np(c): np_C
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np(g): np_G
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# restoration (FFPE)
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restoration: restoration
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restore: restoration
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# methylation (metrics in v2; names mapped already so controls_raw.tsv is labelled consistently)
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bs conversion i c1: bs1_C1
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bs conversion i c2: bs1_C2
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bs conversion i c3: bs1_C3
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bs conversion i c4: bs1_C4
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bs conversion i c5: bs1_C5
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bs conversion i u1: bs1_U1
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bs conversion i u2: bs1_U2
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bs conversion i u3: bs1_U3
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bs conversion i u4: bs1_U4
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bs conversion i u5: bs1_U5
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bs conversion i-c1: bs1_C1
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bs conversion i-c2: bs1_C2
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bs conversion i-c3: bs1_C3
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bs conversion i-c4: bs1_C4
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bs conversion i-c5: bs1_C5
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bs conversion i-c6: bs1_C6
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bs conversion i-u1: bs1_U1
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bs conversion i-u2: bs1_U2
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bs conversion i-u3: bs1_U3
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bs conversion i-u4: bs1_U4
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bs conversion i-u5: bs1_U5
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bs conversion i-u6: bs1_U6
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bs conversion i c6: bs1_C6
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bs conversion i u6: bs1_U6
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bs conversion ii-1: bs2_1
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bs conversion ii-2: bs2_2
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bs conversion ii-3: bs2_3
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bs conversion ii-4: bs2_4
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gt mismatch 1(pm): gtmm_1_pm
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gt mismatch 2(pm): gtmm_2_pm
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gt mismatch 3(pm): gtmm_3_pm
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gt mismatch 4(pm): gtmm_4_pm
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gt mismatch 5(pm): gtmm_5_pm
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gt mismatch 6(pm): gtmm_6_pm
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gt mismatch 1(mm): gtmm_1_mm
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gt mismatch 2(mm): gtmm_2_mm
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gt mismatch 3(mm): gtmm_3_mm
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gt mismatch 4(mm): gtmm_4_mm
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gt mismatch 5(mm): gtmm_5_mm
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gt mismatch 6(mm): gtmm_6_mm
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specificity 1: spec2_1
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specificity 2: spec2_2
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specificity 3: spec2_3
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# Categories treated as methylation-only (dataset type detection, QC-043).
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methylation_categories:
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- bisulfite conversion i
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- bisulfite conversion ii
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- specificity i
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- specificity ii
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# Report exclusion list (QC-010): raw-probe views leave these out; derived metrics still use them.
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report_exclude:
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categories: [negative, norm]
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names: ["np(g) 1", "np(g) 2", "np(g) 3", "np(g) 4", "np(g) 5", "biotin(5k)", "dnp(20k)"]
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