Comments (4)
akiezun
commented on August 23, 2024
The doc is here -it may be easier to edit as a google doc. https://docs.google.com/a/broadinstitute.org/document/d/10j9UvZQ_jOY2vKz59eHrRdrazxHUscs1DnWan5sVTao/edit#
from gatk.
nh13
commented on August 23, 2024
Can someone here take inventory of the various Picard tools that you want to consider moving over? These are NOT represented in the GATK best practices document, for example MergeBamAlignment or ValidateSamFile.
from gatk.
akiezun
commented on August 23, 2024
@nh13 my sense is that most of picard tools (non-private ones) will either be moved over to hellbender or we'll keep linking to picard (but the latter seems suboptimal - there should be just one toolkit)
from gatk.
akiezun
commented on August 23, 2024
this is done
from gatk.
Related Issues (20)
- Using PathSeqFilterSpark --ignore-alignment-contigs raises error
- ApplyVQSR Exception thrown at a/some variation site(s) after INDEL VQSR
- PrintReads introduces N bases when encoding some CRAMs and changes sequence HOT 15
- PostprocessGermlineCNVCalls error HOT 2
- GenotypeGVCFs report java.lang.OutOfMemoryError: Java heap space while call incremental imported GenomicsDB HOT 3
- Prevent users enabling annotations with mismatching data type (flow etc) HOT 7
- VariantAnnotator IndexOutOfBoundsException
- [bug report] CNNScoreVariants can't continue HOT 1
- VCF row validation error on gCNV results HOT 9
- PackagesNotFoundError: The following packages are not available from current channels: HOT 3
- java.lang.IllegalArgumentException: the number of genotypes is too large for ploidy 8 and 55 alleles: approx. 3381098545 HOT 3
- Funcotator - WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr....
- several genes are reported in "PREDICTED_LOF" for a balanced translocation HOT 3
- Docker container should allow use by non-privileged user HOT 2
- Funcotator gnomAD incoherent number of output fields
- CombineGVCFs meet error HOT 2
- Empty BAM after running SplitNCigarReads HOT 4
- Troubleshooting VCF Output Truncation Issue during GATK CombineGVCFs Process HOT 1
- GATK Tutorial#11682 reproduce different results HOT 2
- SoftClippedReadFilter Shows Filtering Result Opposite to Description. HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gatk.