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List key GATK walkers #2

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akiezun opened this issue Dec 10, 2014 · 5 comments
Closed

List key GATK walkers #2

akiezun opened this issue Dec 10, 2014 · 5 comments

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@akiezun
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akiezun commented Dec 10, 2014

Not all walkers will move to hellbender, only those that are most useful and we want to keep supporting. This issue will collect them - they will come from best practices, help forum, talking to dev team members, common sense.
@lbergelson
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Our current working list of important tools: https://docs.google.com/a/broadinstitute.org/document/d/10j9UvZQ_jOY2vKz59eHrRdrazxHUscs1DnWan5sVTao/edit

@akiezun
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akiezun commented Dec 11, 2014

@rpoplin @eitanbanks can you add your favorites here or to the doc?

@ldgauthier
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Two others that I've been using a lot recently from our private repo are AssessNA12878 and CalibrateGenotypeLikelihoods. I use VariantsToTable periodically too.

@ldgauthier
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Right now I am using VariantAnnotator. And it is slow as molasses. It would make me indescribably happy if the new version was at least 50% faster.

@akiezun
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akiezun commented Dec 15, 2014

i'm going to close this. Please add issue per walker

@akiezun akiezun closed this as completed Dec 15, 2014
@droazen droazen mentioned this issue Jun 18, 2015
Closed
@cmnbroad cmnbroad mentioned this issue Dec 8, 2015
Open
@samuelklee samuelklee mentioned this issue Sep 30, 2017
Closed
1 task
@ldgauthier ldgauthier mentioned this issue Dec 8, 2017
Merged
@cmnbroad cmnbroad mentioned this issue Jul 23, 2018
Merged
jonn-smith added a commit that referenced this issue Nov 19, 2018
@jonn-smith
# This is a combination of 2 commits.
05e0c15 
# This is the 1st commit message:

Updated data source inputs to accept NIO paths for backing files.

Now you can specify a URL in the backing file areas of the configuration
files for Funcotator data sources and the backing files will be read by
the FuncotationDataSourceFactories.

This effectively enables use of data sources in the cloud or a mix of
local- and cloud-based data sources through a config file change.

This update will enable gnomAD annotations (once the data sources are
    updated to point at the gnomAD files on Google Cloud).

Added in cloud data sources to test with.

Minor refactoring of LocatableXsvFuncotationFactory.  Now can only
support one file at a time instead of multiple files for each instance.

Fixes #5348

# This is the commit message #2:

Added in more cloud data sources.

New cloud dataset contains local data sources and a pointer to the
gnomAD google cloud bucket.
ldgauthier added a commit that referenced this issue Mar 25, 2019
@ldgauthier
# This is a combination of 3 commits.
b6bb4f2 
# This is the 1st commit message:

Tiny tool to take the smallest interval the spans the given intervals

# This is the commit message #2:

Sort spanning intervals
Start moving the spanning interval determinination into GenomicsDBImport

# This is the commit message #3:

Fix dictionary arg
ldgauthier added a commit that referenced this issue Aug 2, 2019
@ldgauthier
Item #2 -- "Add a simple direct integration test for the new
5fd4d9b 
--floor-blocks HaplotypeCaller arg"
Also clarified beta status for GVCF mode just for Mutect2
ldgauthier added a commit that referenced this issue Aug 5, 2019
@ldgauthier
Item #2 -- "Add a simple direct integration test for the new
0ce6686 
--floor-blocks HaplotypeCaller arg"
Also clarified beta status for GVCF mode just for Mutect2
@samuelklee samuelklee mentioned this issue Sep 18, 2019
Open
@asmirnov239 asmirnov239 mentioned this issue Apr 21, 2020
Merged
@LN908 LN908 mentioned this issue May 19, 2021
Closed
@rsasch rsasch mentioned this issue May 26, 2021
Merged
@rsasch rsasch mentioned this issue Jul 20, 2021
Merged
lucidtronix pushed a commit that referenced this issue Jul 27, 2021
@meganshand
continuous tensor maps made from big query (#2)
f715140
RoriCremer added a commit that referenced this issue Aug 2, 2021
@RoriCremer
Add VAT validation rule #2 [VS-19] (#7374)
b24f091 
* discussed w AH and LL--20 is a better cutoff than 19

* add validation rule 2

* localize template properly

* typo on proj id

* but where should this live?

* use bespoke bcftools docker
rsasch added a commit that referenced this issue Sep 13, 2021
@rsasch
formatting change #2 to sample QC README
dc110b8
RoriCremer pushed a commit that referenced this issue Sep 20, 2021
@rsasch @RoriCremer
formatting change #2 to sample QC README
0f5ed5e
This was referenced Mar 17, 2023
Closed
Closed
@jdjdj0202 jdjdj0202 mentioned this issue May 29, 2023
Closed
rsasch added a commit that referenced this issue Nov 17, 2023
@rsasch
attempt #2 at parameters
a8f46ad
rsasch added a commit that referenced this issue Jan 30, 2024
@rsasch
attempt #2 to fix ClinvarSignificance output
5ef1c51
@yuweibao15 yuweibao15 mentioned this issue Jun 21, 2024
Closed
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3 participants
@akiezun @lbergelson @ldgauthier