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Feature/imputation improvement2#1

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akotlar wants to merge 28 commits intomainbystrogenomics/imputationserver2:mainfrom feature/imputation-improvement2bystrogenomics/imputationserver2:feature/imputation-improvement2Copy head branch name to clipboard

+701-408

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Commits on Oct 19, 2024

• good input_validation_vcf.nf that does the necessary vcf preprocessing and outputs to target output directory

  akotlar

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  4ccb49e

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• fix location of split_vcfs

  akotlar

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  294e3db

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• min_r2 of .8

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  0392fea

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Commits on Oct 20, 2024

• don't split if only 1 chromosome

  akotlar

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  edd0d32

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Commits on Oct 21, 2024

• enable beagle imputation

  akotlar

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  2c3f20c

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• move beagle imputed outputs until we figure out how to concat and get around gaps

  akotlar

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  cd16be9

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• use java default for memory

  akotlar

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  b4907dd

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• cleanup; remove unneeded stuff

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  e801e34

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• allow uncompressed vcfs

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  3e04288

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• don't hardcode paths

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  0c4766e

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Commits on Oct 22, 2024

• point to bystrogenomics host

  akotlar

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  daf97fc

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• sort the files first

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  af3c301

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• don't copy the split_vcfs

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  f608d80

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• add DR2 filter

  akotlar

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  1803027

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• try to index consistently

  akotlar

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  05cf56b

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• attempt to make csi go to the output dir

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  5845968

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• format

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  a7089ce

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• format and improve merging of outputs

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  3794035

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• avoid sort when concatenating

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  2ade87a

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• drop exact match duplicates only

  akotlar

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  8edfbd4

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• fix eagle

  akotlar

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  5becc02

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• streamline concat/norm in beagle imputation; add main.config

  akotlar

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  b78d520

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• make final indexing optional

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  7dfce22

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• don't index final output

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  41f036e

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• more threads for beagle

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  26c183b

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Commits on Oct 23, 2024

• cleanup

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  5ffd5cf

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• cleanup

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  5788337

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Commits on Oct 24, 2024

• don't try to cleanup; won't work anyway

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  82622e0

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