Comments (2)
etal
commented on August 13, 2024
Sure it does, at least if the input BED file also contains a "name" field in the 4th column.
$ more some-targets.bed
chr1 30330 30540 MIR1302-10
chr1 35051 35290 FAM138A
chr1 35290 35529 FAM138A
chr1 35623 35833 FAM138A
chr1 69039 69294 OR4F5
chr1 69294 69549 OR4F5
chr1 69549 69804 OR4F5
chr1 69804 70059 OR4F5
chr1 367618 367873 OR4F16
chr1 367873 368128 OR4F16
$ samtools bedcov -Q 1 some-targets.bed some-reads.bam
chr1 30330 30540 MIR1302-10 0
chr1 35051 35290 FAM138A 0
chr1 35290 35529 FAM138A 50
chr1 35623 35833 FAM138A 0
chr1 69039 69294 OR4F5 0
chr1 69294 69549 OR4F5 1228
chr1 69549 69804 OR4F5 748
chr1 69804 70059 OR4F5 0
chr1 367618 367873 OR4F16 0
chr1 367873 368128 OR4F16 0
$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd
...
from cnvkit.
johnmu
commented on August 13, 2024
Ah I see, yeah my BED file was missing the 4th column. Thanks!
from cnvkit.
Related Issues (20)
- Targets: 3948 (1.4789%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) HOT 3
- Docker needed HOT 2
- Examining conflicts takes forever installing cnvkit with conda HOT 3
- genemetrics result different between 0.9.8 and 0.9.9 HOT 1
- Bias corrections
- Setting arbitrary bin size for WGS data HOT 3
- Can't convert to gistic marker due to input validation HOT 4
- Runtime error while running batch process HOT 6
- AttributeError: 'Namespace' object has no attribute 'func' HOT 1
- Could not retrieve index file for CRAM files
- How to integrate the copy numbers of gene.
- batch creates FASTA's bed in working dir not in output-dir
- make command failed in /test folder HOT 2
- KeyError: '1 not in /home/renoguch/hg19/hg19.fa.'
- Optionally consider PAR1/2 as diploid in male samples due to reference genome masking HOT 3
- Different sex estimated from cnr and cns files
- GISTIC overlapp issue
- Incremental reference Generation HOT 1
- create reference from affected only and no bait files HOT 1
- How to find out the version of cnvkit installed on my computer? 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 cnvkit.