Comments (2)
Idea for arguments:
--maf
: min population allele frequency (default = 0.0)--mad
: min population allele depth (default = 0)--ind-maf
: min individual allele frequency (default = 0.1)--ind-mad
: min individual allele depth (default = 3)--ind-min
: min number of individuals passing--ind-maf
and--ind-mad
(default = 1)
All filters are combined (intersection). This gives good flexibility and makes few assumptions about population size/structure for defaults.
from mchap.
Fixed in #169
from mchap.
Related Issues (20)
- Dockerfile HOT 1
- Avoid integer overflow when calculating unique number of haplotypes
- Table with likelihood of membership of a read in an allele HOT 1
- Filtering options or tool HOT 1
- Report posterior probability of allele presence HOT 1
- Improve error messages for uncompressed and non-indexed input files. HOT 3
- Allow multiple readgroups for a single sample HOT 1
- Allow masking of SNV reference alleles
- Improve CRAM performance by passing reference fasta HOT 1
- Replace `--skip-rare-haplotypes` with a generic `--filter-haplotypes` argument. HOT 2
- Allow setting of precision for floats in VCF
- Improve defaults for find-snvs HOT 1
- Avoid holding alignment file handles open. HOT 1
- Additional info fields
- Correct usage of `AN` field
- Improve error messages for mismatching Reference/VCF/BAM
- version HOT 1
- Sparse representation of genotype posterior HOT 1
- Consider replacing `ADMF` with `AF` in find-snvs output
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 mchap.