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Grafpop&CHARR #7

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Grafpop&CHARR #7

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Commits on Nov 29, 2023

  1. Merge branch 'infer_sex_ancestry' of https://github.com/vanallenlab/p… 

    …ancan_germline_wgs into infer_sex_ancestry
    Noah Fields committed Nov 29, 2023
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Commits on Nov 30, 2023

  1. small edits to sex_infer.R round 2

    Noah Fields committed Nov 30, 2023
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  2. small edits to sex_infer.R updated logic

    Noah Fields committed Nov 30, 2023
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Commits on Dec 7, 2023

  1. new Dockerfile as well as corresponding wdl

    Noah Fields committed Dec 7, 2023
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  2. increasing memory slightly on for ancestry inference

    Noah Fields committed Dec 7, 2023
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Commits on Dec 8, 2023

  1. Small edit to infer_sex.R to be more robust

    Noah Fields committed Dec 8, 2023
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  2. another small change to infer_sex.R

    Noah Fields committed Dec 8, 2023
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Commits on Jan 5, 2024

  1. Add wdl to transfer files to GCS automatically

    Noah Fields committed Jan 5, 2024
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Commits on Jan 12, 2024

  1. adding for purposes of usability of grafpop results

    Noah Fields committed Jan 12, 2024
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  2. chmod a file

    Noah Fields committed Jan 12, 2024
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  3. chmod a file update

    Noah Fields committed Jan 12, 2024
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Commits on Jan 13, 2024

  1. fixed error in sex_infer.R

    Noah Fields committed Jan 13, 2024
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Commits on Jan 23, 2024

  1. added some helper functions

    Noah Fields committed Jan 23, 2024
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Commits on Jan 25, 2024

  1. added an automatic converter for json file formats

    Noah Fields committed Jan 25, 2024
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Commits on Jan 29, 2024

  1. added charr Dockerfile

    Noah Fields committed Jan 29, 2024
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  2. edited charr Dockerfile

    Noah Fields committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. edited charr dockerfile

    Noah Fields committed Jan 30, 2024
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  2. edited charr dockerfile

    Noah Fields committed Jan 30, 2024
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  3. adding echtvar

    Noah Fields committed Jan 30, 2024
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  4. adding echtvar

    Noah Fields committed Jan 30, 2024
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  5. updated json_converter.py; works now

    Noah Fields committed Jan 30, 2024
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Commits on Jan 31, 2024

  1. bcftools docker added

    Noah Fields committed Jan 31, 2024
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  2. bcftools docker edited

    Noah Fields committed Jan 31, 2024
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  3. bcftools docker edited

    Noah Fields committed Jan 31, 2024
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  4. edit bcftool docker

    Noah Fields committed Jan 31, 2024
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  5. edit bcftool docker

    Noah Fields committed Jan 31, 2024
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  6. edit bcftool docker

    Noah Fields committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. added file for echtvar

    Noah Fields committed Feb 1, 2024
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  2. added bcftools to charr docker

    Noah Fields committed Feb 1, 2024
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  3. edited charr docker

    Noah Fields committed Feb 1, 2024
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  4. edited charr docker

    Noah Fields committed Feb 1, 2024
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  5. edited charr docker

    Noah Fields committed Feb 1, 2024
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  6. edited charr docker

    Noah Fields committed Feb 1, 2024
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  7. edited charr docker

    Noah Fields committed Feb 1, 2024
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  8. edited charr docker

    Noah Fields committed Feb 1, 2024
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Commits on Feb 5, 2024

  1. updated WGSFastqToCram wdl

    Noah Fields authored and Noah Fields committed Feb 5, 2024
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Commits on Feb 7, 2024

  1. No more raw gvcfs being transferred

    Noah Fields authored and Noah Fields committed Feb 7, 2024
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  2. small edit to G2C transfer file wdl

    Noah Fields authored and Noah Fields committed Feb 7, 2024
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Commits on Feb 16, 2024

  1. bcftools docker

    Noah Fields authored and Noah Fields committed Feb 16, 2024
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Commits on Feb 26, 2024

  1. added grafpop and charr wdls

    Noah Fields committed Feb 26, 2024
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  2. Delete scripts/gsi_helpers/data/gsc.tsv

    @noahfields1
    noahfields1 authored Feb 26, 2024
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  3. Delete scripts/gsi_helpers/data/gsc_filtered.tsv

    @noahfields1
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  4. Delete scripts/gsi_helpers/data/gsc_filtered_test_genes.tsv

    @noahfields1
    noahfields1 authored Feb 26, 2024
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  5. Delete scripts/gsi_helpers/data/.DS_Store

    @noahfields1
    noahfields1 authored Feb 26, 2024
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Commits on Mar 4, 2024

  1. Added analysis for GSC study

    Noah Fields committed Mar 4, 2024
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Commits on Mar 7, 2024

  1. Adding case-control matching for AoU UFC study

    Noah Fields committed Mar 7, 2024
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  2. update to matching algorithm

    Noah Fields committed Mar 7, 2024
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Commits on Mar 11, 2024

  1. Added code to consolidate data

    Noah Fields authored and Noah Fields committed Mar 11, 2024
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Commits on Mar 21, 2024

  1. added some new WDLs

    Noah Fields committed Mar 21, 2024
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  2. small adjustments to aou_charr.wdl

    Noah Fields committed Mar 21, 2024
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Commits on Mar 25, 2024

  1. added a VEP_hg19 version that is bad practice

    Noah Fields committed Mar 25, 2024
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  2. added edit to bad practice Vep hg19 wdl

    Noah Fields committed Mar 25, 2024
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  3. editing hg19 Vep

    Noah Fields committed Mar 25, 2024
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  4. editing hg19 Vep

    Noah Fields committed Mar 25, 2024
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  5. editing hg19 Vep

    Noah Fields committed Mar 25, 2024
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  6. editing hg19 Vep

    Noah Fields committed Mar 25, 2024
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  7. editing hg19 Vep

    Noah Fields committed Mar 25, 2024
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  8. adding new hg19 Vep

    Noah Fields committed Mar 25, 2024
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  9. adding new hg19 Vep

    Noah Fields committed Mar 25, 2024
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  10. adding new hg19 Vep

    Noah Fields committed Mar 25, 2024
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  11. edit hg19 Vep

    Noah Fields committed Mar 25, 2024
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  12. edit hg19 Vep

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Commits on Mar 26, 2024

  1. edit hg19 Vep

    Noah Fields committed Mar 26, 2024
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  2. edit VEP_hg19

    Noah Fields committed Mar 26, 2024
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  3. edit VEP_hg19

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  4. edit VEP_hg19

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  5. edit VEP_hg19

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  6. edit VEP_hg19

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  7. edit VEP_hg19

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Commits on Mar 27, 2024

  1. edit VEP_hg19.wdl

    Noah Fields committed Mar 27, 2024
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  2. edit VEP_hg19.wdl

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  3. edit VEP_hg19.wdl

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Commits on Mar 28, 2024

  1. edit VEP_hg19.wdl

    Noah Fields committed Mar 28, 2024
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  2. edit VEP_hg19.wdl

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  3. edit VEP_hg19.wdl

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  4. edit VEP_hg19.wdl

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  5. edit VEP_hg19.wdl

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  6. edit VEP_hg19.wdl

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  7. edit VEP_hg19.wdl

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  8. edit VEP_hg19.wdl

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  9. edit VEP_hg19.wdl

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  10. edit VEP_hg19.wdl

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  11. edit VEP_hg19.wdl

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Commits on Mar 29, 2024

  1. edit VEP_hg19.wdl

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  2. edit VEP_hg19.wdl

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Commits on Apr 3, 2024

  1. added method to annotate gsc tsv

    Noah Fields committed Apr 3, 2024
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Commits on Apr 10, 2024

  1. add some wdls

    Noah Fields committed Apr 10, 2024
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  2. edited wdls

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  3. edited wdls

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  4. edited wdls

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  5. edited wdls

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  6. edited wdls

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  7. edited wdls

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  8. edited wdls

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  9. edited wdls

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Commits on Apr 11, 2024

  1. edited wdls

    Noah Fields committed Apr 11, 2024
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  2. edited wdls

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  3. edited wdls

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  4. edited wdls

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  5. edited wdls

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Commits on Apr 16, 2024

  1. edited GSC_CC wdl

    Noah Fields committed Apr 16, 2024
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  2. edited GSC_CC wdl

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Commits on Apr 19, 2024

  1. new edit to cohort_data_qc wdl

    Noah Fields committed Apr 19, 2024
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Commits on Apr 23, 2024

  1. updated germline somatic convergence

    Noah Fields authored and Noah Fields committed Apr 23, 2024
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  2. updated cohort metrics wdl

    Noah Fields authored and Noah Fields committed Apr 23, 2024
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Commits on May 1, 2024

  1. added new wdls and changed some names

    Noah Fields committed May 1, 2024
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  2. edited nc somatic wdl

    Noah Fields committed May 1, 2024
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  3. edited nc somatic wdl

    Noah Fields committed May 1, 2024
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  4. edited nc somatic wdl

    Noah Fields committed May 1, 2024
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  5. edited nc somatic wdl

    Noah Fields committed May 1, 2024
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  6. edited nc somatic wdl

    Noah Fields committed May 1, 2024
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Commits on May 3, 2024

  1. small edit to somatic noncoding gsc

    Noah Fields committed May 3, 2024
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Commits on May 13, 2024

  1. updated wdls

    Noah Fields committed May 13, 2024
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  2. updated wdls

    Noah Fields committed May 13, 2024
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Commits on May 17, 2024

  1. generate sample map wdl

    Noah Fields authored and Noah Fields committed May 17, 2024
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Commits on Jul 24, 2024

  1. changed capitalization error in Coding_Convergence.gsc.wdl

    Noah Fields authored and Noah Fields committed Jul 24, 2024
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  2. small syntax error

    Noah Fields authored and Noah Fields committed Jul 24, 2024
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Commits on Jul 26, 2024

  1. small edit to gsc

    Noah Fields committed Jul 26, 2024
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  2. small edit to gsc

    Noah Fields committed Jul 26, 2024
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  3. fixed convergence

    Noah Fields committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. added hail_rf docker

    Noah Fields committed Jul 29, 2024
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  2. edited hail_rf docker

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  3. edited hail_rf docker

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Commits on Jul 30, 2024

  1. change file name

    Noah Fields authored and Noah Fields committed Jul 30, 2024
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Commits on Aug 7, 2024

  1. added pydata stack docker

    Noah Fields committed Aug 7, 2024
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  2. added pydata stack docker

    Noah Fields committed Aug 7, 2024
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  3. added pydata stack docker

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Commits on Sep 25, 2024

  1. new docker container: gsc_pytools

    Noah Fields committed Sep 25, 2024
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  2. new docker container: gsc_pytools

    @fieldsnoa
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  3. new docker container: gsc_pytools

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  4. new docker container: gsc_pytools

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  5. new docker container: gsc_pytools

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  6. new docker container: gsc_pytools

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  7. new docker container: gsc_pytools

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  8. new docker container: gsc_pytools

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  9. new docker container: gsc_pytools

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  10. new docker container: gsc_pytools

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  11. new docker container: gsc_pytools

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  12. new docker container: gsc_pytools

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  13. new docker container: gsc_pytools

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  14. new docker container: gsc_pytools

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  15. added statsmodels to docker container

    Noah Fields committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. small fix

    Noah Fields committed Sep 26, 2024
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  2. small fix

    Noah Fields committed Sep 26, 2024
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  3. small change in mutation freq calc

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  4. trying to add firthlogist

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  5. switching to python3.9 for firthlogist

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  6. switching to python3.9 for firthlogist

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  7. switching to python3.9 for firthlogist

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  8. switching to python3.9 for firthlogist

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  9. small edit to fishers exact logic

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  10. including firth logistic regression

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  11. including firth logistic regression

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  12. fixing gsc_pytools docker

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  13. fixing gsc_pytools docker

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  14. fixing gsc_pytools docker

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  15. fixing gsc_pytools docker

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  16. fixing gsc_pytools docker

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  17. overhaul to firthLogist

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  18. overhaul to firthLogist

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  19. trying to get firthLogist to converge

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Commits on Sep 27, 2024

  1. adjustment to firth logistic regression parameter options

    @fieldsnoa
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  2. small edit to gsc_util.py

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  3. small edit in the case snp is not in df

    Noah Fields committed Sep 27, 2024
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  4. small capitalization error

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Commits on Sep 28, 2024

  1. small python edit

    Noah Fields committed Sep 28, 2024
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  2. revert to earlier

    Noah Fields authored and Noah Fields committed Sep 28, 2024
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Commits on Sep 30, 2024

  1. added functionality for meta anlysis

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  2. added functionality for meta anlysis

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  3. added functionality for meta anlysis

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  4. added functionality for meta anlysis

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  5. added functionality for meta anlysis

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  6. added some graphing functions

    @fieldsnoa
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  7. graphing fixes

    Noah Fields committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. small edits

    Noah Fields committed Oct 1, 2024
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  2. small edits

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  3. edit to graphing

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  4. small graph edit

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Commits on Oct 2, 2024

  1. edit to meta analysis p_val calc

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  2. edit to p_val calc

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Commits on Oct 3, 2024

  1. implemented FDR for graphing

    @fieldsnoa
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  2. edits to allele freq calc

    @fieldsnoa
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  3. fixing AF

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  4. small bug

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Commits on Oct 4, 2024

  1. fixed FDR problem

    @fieldsnoa
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Commits on Oct 15, 2024

  1. firth fallback implemented

    @fieldsnoa
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  2. firth fallback implemented

    @fieldsnoa
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  3. firth fallback implemented

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  4. firth fallback implemented

    @fieldsnoa
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  5. firth fallback implemented

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  6. firth fallback implemented

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  7. firth fallback implemented

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  8. firth fallback implemented

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Commits on Oct 16, 2024

  1. added seaborn to pydata_stack

    @fieldsnoa
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  2. new ufc docker

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  3. small error in g2c_ufc

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Commits on Oct 17, 2024

  1. fixed firth fallback

    @fieldsnoa
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  2. edit to firth fallback

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Commits on Oct 18, 2024

  1. updated for all gsc contexts

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  2. small update

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  3. small update

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Commits on Oct 23, 2024

  1. simplified analysis in WDL

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  2. simplified analysis in WDL

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  3. simplified analysis in WDL

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  4. simplified analysis in WDL

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  5. simplified analysis in WDL

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  6. simplified analysis in WDL

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Commits on Oct 24, 2024

  1. simplified analysis in WDL

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  2. simplified analysis in WDL

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Commits on Oct 25, 2024

  1. simplified analysis in WDL

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Commits on Oct 29, 2024

  1. added new covariates for HMF

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  2. added primary 1 hot variate for HMF

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Commits on Nov 6, 2024

  1. new covariates for PROFILE log reg analysis

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  2. edited graph function

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Commits on Nov 13, 2024

  1. small edits to graph making

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Commits on Nov 14, 2024

  1. small edits to graph making

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Commits on Nov 15, 2024

  1. added GWAS miniplots

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  2. fixed plotting error

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Commits on Nov 18, 2024

  1. fixed plotting errors. and missing kidney data

    @fieldsnoa
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Commits on Nov 19, 2024

  1. fixed plotting errors.

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  2. fixed plotting errors. i think

    @fieldsnoa
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Commits on Nov 20, 2024

  1. fixed some plotting errors. Legend still needs love.

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  2. Added in cancer_type as covariate for pancancer log-reg model. Volcan… 

    …o Plot Legend still needs love.
    @fieldsnoa
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  3. Added in profile germline coding. Volcano Plot Legend still needs love.

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Commits on Nov 21, 2024

  1. Added in profile germline coding. Volcano Plot Legend still needs love.

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  2. Profile coding coding interaction stats printed out. Needs some qc ap… 

    …parently
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Commits on Dec 2, 2024

  1. Altered way we call germline coding variants

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  2. Altered way we call germline coding variants

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  3. Altered way we call germline coding variants

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  4. Altered way we call germline coding variants

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Commits on Dec 6, 2024

  1. added qqman package to g2c_ufc

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  2. added qqman

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  3. added qqman

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  4. added qqman

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  5. added qqman

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  6. added qqman

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  7. added qqman

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  8. added qqman

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  9. added qqman

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  10. added qqman

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  11. added qqman

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Commits on Dec 10, 2024

  1. retrying qqman docker

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  2. retrying qqman docker

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    fieldsnoa committed Dec 10, 2024
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  3. retrying qqman docker

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    fieldsnoa committed Dec 10, 2024
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  4. retrying qqman docker

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    fieldsnoa committed Dec 10, 2024
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  5. retrying qqman docker

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    fieldsnoa committed Dec 10, 2024
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Commits on Dec 11, 2024

  1. retrying qqman docker

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    fieldsnoa committed Dec 11, 2024
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  2. retrying qqman docker

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    fieldsnoa committed Dec 11, 2024
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  3. retrying qqman docker

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    fieldsnoa committed Dec 11, 2024
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