# samtools

**Repository Path**: mingyangde/samtools

## Basic Information

- **Project Name**: samtools
- **Description**: Tools (written in C using htslib) for manipulating next-generation sequencing data
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 1
- **Created**: 2020-07-22
- **Last Updated**: 2020-12-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

samtools
========

[![Build Status](https://travis-ci.org/samtools/samtools.svg?branch=develop)](https://travis-ci.org/samtools/samtools)
[![Build status](https://ci.appveyor.com/api/projects/status/enujqi06jlqw493t/branch/develop?svg=true)](https://ci.appveyor.com/project/samtools/samtools/branch/develop)
[![Github All Releases](https://img.shields.io/github/downloads/samtools/samtools/total.svg)](https://github.com/samtools/samtools/releases/latest)

This is the official development repository for samtools.

The original samtools package has been split into three separate
but tightly coordinated projects:
- [htslib](https://github.com/samtools/htslib): C-library for handling high-throughput sequencing data
- samtools: mpileup and other tools for handling SAM, BAM, CRAM
- [bcftools](https://github.com/samtools/bcftools): calling and other tools for handling VCF, BCF

See also http://github.com/samtools/

### Building Samtools

See [INSTALL](INSTALL) for complete details.
[Release tarballs][download] contain generated files that have not been
committed to this repository, so building the code from a Git repository
requires extra steps:

```sh
autoheader            # Build config.h.in (this may generate a warning about
                      # AC_CONFIG_SUBDIRS - please ignore it).
autoconf -Wno-syntax  # Generate the configure script
./configure           # Needed for choosing optional functionality
make
make install
```

By default, this will build against an HTSlib source tree in `../htslib`.
You can alter this to a source tree elsewhere or to a previously-installed
HTSlib by configuring with `--with-htslib=DIR`.

[download]: http://www.htslib.org/download/