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config.yaml
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config.yaml
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raw:
plink:
contigs:
# For UKB chromosome codes, see:
# https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=531
# "numeric chromosome label 1-26; 23=X,24=Y,25=XY,26=MT"
- {index: 0, code: 1, name: 1}
- {index: 1, code: 2, name: 2}
- {index: 2, code: 3, name: 3}
- {index: 3, code: 4, name: 4}
- {index: 4, code: 5, name: 5}
- {index: 5, code: 6, name: 6}
- {index: 6, code: 7, name: 7}
- {index: 7, code: 8, name: 8}
- {index: 8, code: 9, name: 9}
- {index: 9, code: 10, name: 10}
- {index: 10, code: 11, name: 11}
- {index: 11, code: 12, name: 12}
- {index: 12, code: 13, name: 13}
- {index: 13, code: 14, name: 14}
- {index: 14, code: 15, name: 15}
- {index: 15, code: 16, name: 16}
- {index: 16, code: 17, name: 17}
- {index: 17, code: 18, name: 18}
- {index: 18, code: 19, name: 19}
- {index: 19, code: 20, name: 20}
- {index: 20, code: 21, name: 21}
- {index: 21, code: 22, name: 22}
- {index: 22, code: 23, name: X}
- {index: 23, code: 24, name: Y}
- {index: 24, code: 25, name: XY}
- {index: 25, code: 26, name: MT}
bgen:
contigs:
# Same as PLINK w/o Y and MT
# See http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=263 for
# details on `n_consent_samples` which is "number of linked samples
# (i.e.currently consenting participants) in dataset" used in
# .sample file names. To find number of variants, use:
# for f in `gsutil ls gs://rs-ukb/raw-data/gt-imputation/*.txt`; do
# echo $f `gsutil cat $f | wc -l`; done
- {index: 0, code: 1, name: 1, n_consent_samples: 487296, n_variants: 7402791}
- {index: 1, code: 2, name: 2, n_consent_samples: 487296, n_variants: 8129063}
- {index: 2, code: 3, name: 3, n_consent_samples: 487296, n_variants: 6696680}
- {index: 3, code: 4, name: 4, n_consent_samples: 487296, n_variants: 6555871}
- {index: 4, code: 5, name: 5, n_consent_samples: 487296, n_variants: 6070641}
- {index: 5, code: 6, name: 6, n_consent_samples: 487296, n_variants: 5751712}
- {index: 6, code: 7, name: 7, n_consent_samples: 487296, n_variants: 5405524}
- {index: 7, code: 8, name: 8, n_consent_samples: 487296, n_variants: 5282223}
- {index: 8, code: 9, name: 9, n_consent_samples: 487296, n_variants: 4066774}
- {index: 9, code: 10, name: 10, n_consent_samples: 487296, n_variants: 4562904}
- {index: 10, code: 11, name: 11, n_consent_samples: 487296, n_variants: 4628348}
- {index: 11, code: 12, name: 12, n_consent_samples: 487296, n_variants: 4431052}
- {index: 12, code: 13, name: 13, n_consent_samples: 487296, n_variants: 3270217}
- {index: 13, code: 14, name: 14, n_consent_samples: 487296, n_variants: 3037521}
- {index: 14, code: 15, name: 15, n_consent_samples: 487296, n_variants: 2767971}
- {index: 15, code: 16, name: 16, n_consent_samples: 487296, n_variants: 3089612}
- {index: 16, code: 17, name: 17, n_consent_samples: 487296, n_variants: 2660711}
- {index: 17, code: 18, name: 18, n_consent_samples: 487296, n_variants: 2599579}
- {index: 18, code: 19, name: 19, n_consent_samples: 487296, n_variants: 2087017}
- {index: 19, code: 20, name: 20, n_consent_samples: 487296, n_variants: 2082571}
- {index: 20, code: 21, name: 21, n_consent_samples: 487296, n_variants: 1261158}
- {index: 21, code: 22, name: 22, n_consent_samples: 487296, n_variants: 1255683}
- {index: 22, code: 23, name: X, n_consent_samples: 486645, n_variants: 3917799}
- {index: 24, code: 25, name: XY, n_consent_samples: 486331, n_variants: 45906}