Comments (4)
nh13
commented on July 22, 2024
Take a look at the ValidateSamFile tool within Picard: http://broadinstitute.github.io/picard/.
Here's a link to the tool's documentation:
http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile
from htsjdk.
chilinglam
commented on July 22, 2024
@nh13 , thank you for the information. I wonder if it is possible to validate the BAI file as well? The VadliateSamFile seems to take only the BAM file for validation.
from htsjdk.
nh13
commented on July 22, 2024
Ah, sorry, you can use the VALIDATE_INDEX option with the ValidateSamFile tool.
Also, please post general questions to [email protected], and we can use this for bug reports and feature requests.
from htsjdk.
chilinglam
commented on July 22, 2024
Thank you for your help @nh13!
I will use the [email protected] next time. Sorry about that.
from htsjdk.
Related Issues (20)
- Race conditions accessing CRAM's reference data through ReferenceSource
- Add a better error message when the reference is too long for indexing HOT 5
- Question: Tabix index to find min(POS) and max(POS) in each contig
- Histogram class uses unsafe methods for returning min/max
- CRAM: 8-Bin Base Quality Compression HOT 1
- SamReader slower than expected on network drive HOT 1
- Escaped doublequotes in INFO descriptions result in invalid VCF file HOT 2
- Question: How to generate FAI files and TBI files HOT 5
- SamReaderFactory should use current defaults when makeDefault() is called
- Error when reading a VCF 4.3 file with spaces in INFO field values HOT 1
- htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions HOT 1
- SAMFileWriterFactory creates .bai file when writing .cram file HOT 1
- Deleted Java developers team
- IOUtil.openFileForMd5CalculatingWriting() puts the md5 file in the wrong place.
- support for Azure blob storage? (specifically access to BAM/CRAM files in Azure blob storage by IGV)
- VariantContext has inconsistent behavior on getting allele type with spanning deletions
- Resolve issues around integrating HTTP NIO provider
- Truncation issue with GZIPInputStream when reading bgzip-compressed streams HOT 1
- Ambiguous assertions in the tests HOT 1
- Iterator not working on vcffileReader HOT 3
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 htsjdk.