VcfStats

License	MIT
Categories	FST Data Data Formats Serialization
GroupId	com.github.biopet
ArtifactId	vcfstats_2.11
Last Version	1.2
Release Date	Jul 16, 2018
Type	jar
Description	VcfStats VcfStats
Project URL	https://github.com/biopet/vcfstats
Project Organization	Biopet
Source Code Management	https://github.com/biopet/vcfstats

Download vcfstats_2.11

Filename	Size
vcfstats_2.11-1.2.pom
vcfstats_2.11-1.2.jar	173 KB
vcfstats_2.11-1.2-sources.jar	12 KB
vcfstats_2.11-1.2-javadoc.jar	379 KB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/com.github.biopet/vcfstats_2.11/ -->
<dependency>
    <groupId>com.github.biopet</groupId>
    <artifactId>vcfstats_2.11</artifactId>
    <version>1.2</version>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/com.github.biopet/vcfstats_2.11/
implementation 'com.github.biopet:vcfstats_2.11:1.2'

Gradle Kotlin

// https://jarcasting.com/artifacts/com.github.biopet/vcfstats_2.11/
implementation ("com.github.biopet:vcfstats_2.11:1.2")

Apache Buildr

'com.github.biopet:vcfstats_2.11:jar:1.2'

Apache Ivy

<dependency org="com.github.biopet" name="vcfstats_2.11" rev="1.2">
  <artifact name="vcfstats_2.11" type="jar" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='com.github.biopet', module='vcfstats_2.11', version='1.2')
)

Scala SBT

libraryDependencies += "com.github.biopet" % "vcfstats_2.11" % "1.2"

Leiningen

[com.github.biopet/vcfstats_2.11 "1.2"]

Dependencies

compile (3)

Group / Artifact	Type	Version
org.scala-lang : scala-library	jar	2.11.12
com.github.biopet : tool-utils_2.11	jar	0.4
com.github.biopet : spark-utils_2.11	jar	0.4

provided (2)

Group / Artifact	Type	Version
org.apache.spark : spark-core_2.11	jar	2.3.0
org.apache.spark : spark-sql_2.11	jar	2.3.0

test (1)

Group / Artifact	Type	Version
com.github.biopet : tool-test-utils_2.11	jar	0.2.2

Project Modules

There are no modules declared in this project.

VcfStats

Vcfstats is a tool that can generate metrics from a vcf file.

• General stats (default, can be disabled)
• Genotype stats (default, can be disabled)
• Sample compare (default, can be disabled)
• Sample distributions (default, can be disabled)
• Field histograms

This tool can run locally single threaded but also on a Apache Spark cluster.

Documentation

For documentation and manuals visit our github.io page.

About

VcfStats is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contact

For any question related to VcfStats, please use the github issue tracker or contact the SASC team directly at: [email protected].

Biopet

Versions

Version
1.2 Jul 16, 2018
1.1 Feb 27, 2018
1.0 Dec 5, 2017