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  • test: update test scaffold for autogenerated vcfs

    @markwoon markwoon committed May 19, 2021
    90758c8

  • docs: add test details

    @markwoon markwoon committed Apr 22, 2021
    1acbab2

  • docs: initial doc on testing

    @markwoon markwoon committed Apr 22, 2021
    efbb79c

  • chore: clean up

    @BinglanLi BinglanLi committed Apr 14, 2021
    6f6f83e

  • fix: fix bad reference base for deletion in example VCF

    @whaleyr whaleyr committed Apr 5, 2021
    697b43f

  • docs: update instructions for how to run PharmCAT components

    @whaleyr whaleyr committed Apr 5, 2021
    e71ba97

  • docs: remove CLI flag for PharmCAT that's been removed from code

    @whaleyr whaleyr committed Apr 2, 2021
    9a1c43d

  • docs: update CLI options for PharmCAT jar

    @whaleyr whaleyr committed Apr 1, 2021
    e4c3900

  • chore: update gradle tasks for generating intervals and positions files - add new intervals file generator - add version suffix to positions file

    @whaleyr whaleyr committed Apr 1, 2021
    a970111

  • add descriptions of the GATK LiftoverVcf tool functions.

    @BinglanLi BinglanLi committed Mar 31, 2021
    e87de0c

  • Updated Preparing VCF Files (markdown)

    @BinglanLi BinglanLi committed Mar 31, 2021
    4182ed6

  • update liftover using the GATK tool

    @BinglanLi BinglanLi committed Mar 31, 2021
    4f955c0

  • fix - extract PGx positions right after VCF normalization

    @BinglanLi BinglanLi committed Mar 29, 2021
    f3a2528

  • doc: update python package requirements

    @BinglanLi BinglanLi committed Mar 20, 2021
    e812410

  • Updated VCF preprocessing doc according to the latest feat

    @BinglanLi BinglanLi committed Mar 19, 2021
    a010704

  • update the content in the Preprocess-VCF-Files-Using-PharmCAT.md add disclaimer on the top

    @BinglanLi BinglanLi committed Feb 20, 2021
    bb5ae66

  • squash bad char

    @markwoon markwoon committed Feb 11, 2021
    6e1e52e

  • Updated Preparing VCF Files (markdown)

    @BinglanLi BinglanLi committed Jan 8, 2021
    8442d4a

  • Add example command for generating intervals

    @whaleyr whaleyr committed May 7, 2020
    0e04214

  • Update wording for reference allele requiremnts

    @whaleyr whaleyr committed May 7, 2020
    ba404ba

  • Update docs about chromosomal intervals

    @whaleyr whaleyr committed Feb 25, 2020
    10e97fd

  • Improve "Running" docs based on user feedback

    @whaleyr whaleyr committed Nov 21, 2019
    a8ddcac

  • Change from "Astrolabe" to "OutsideCall" - refactor all the Astrolabe-specific references to "Outside Call" instead - we want to enable calls from any outside source that can supply their result in TSV-formatted files - Astrolabe is still used as a default example and we other calls to follow their format

    @whaleyr whaleyr committed Oct 8, 2019
    632693b

  • Make response clearer.

    @markwoon markwoon committed Apr 9, 2019
    a7e4d37

  • Add FAQ page.

    @markwoon markwoon committed Apr 9, 2019
    0e60b94

  • Tweak sentence.

    @markwoon markwoon committed Apr 9, 2019
    f0a2b57

  • Updated Home (markdown)

    @mwcarrillo mwcarrillo committed Jan 9, 2019
    bcd8e60

  • Fix mentions of "pipeline" to "tool" - PharmCAT is not a pipeline, it's a tool that fits into a larger pipeline

    @whaleyr whaleyr committed Oct 26, 2018
    79f5743

  • Remove more unneeded wiki pages * info is out-of-date and unneeded

    @whaleyr whaleyr committed May 21, 2018
    93af16c

  • Update PharmCAT wiki * add an example VCF file for reference * better separate the content of VCF requirements and VCF preparation examples * clarify the insertion/deletion requirements and add helpful examples * remove all references to the Docker preprocessor (no longer available) * reorganize the homepage to make it more coherent

    @whaleyr whaleyr committed May 21, 2018
    aa22045