Comments (3)
AFAICT from the documentation, Picard does not seem to provide the capability to run on restricted regions like samtools or GATK. Some tools can take an intervals file but that's not the same thing.
@nh13 Can you please confirm or provide a correction?
from picard.
You are correct that this functionality does not exist in ViewSam
and not all tools take interval lists. It would not be hard to add a command line option to ViewSam
to subset to a specific region.
from picard.
I'll put in a feature request for this.
from picard.
Related Issues (20)
- BUILD FAILED error HOT 1
- Mark Duplicates - Not Enough Fields Exception HOT 2
- Samtofastq does not retain all the information HOT 5
- Picard build failed HOT 1
- PICARD termination , HOT 2
- BedToIntervalList reportedly does not handle stdin properly HOT 2
- Inconsistencies in Picard MarkDuplicates Histogram Data Output HOT 2
- picard markduplicate issue HOT 2
- Guide to Installing OpenJDK Version 1.8.0_352 on Ubuntu for Picard Tool Compatibility HOT 1
- Conda installer HOT 8
- Picard Cloud HOT 2
- Creating HOT 1
- Installation problem of v3.1.0 HOT 4
- Question marks in output of Picard tools HOT 5
- --TMP_DIR parameter is ignored and tmp dir defaults to /tmp for CollectInsertSizeMetrics (and possibly more picard tools)) HOT 1
- unable to run picard HOT 2
- INVALID_ALIGNMENT_START HOT 4
- BedToIntervalList doesn't handle empty bed region edge cases properly HOT 8
- java.io.FileNotFoundException: /tmp/CSPI.tmp15948393444880722616/7573.tmp (Too many open files) HOT 1
- warning: unable to load libgkl_compression.so from native/libgkl_compression.so (permission denied)
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 picard.