Skip to main content
Warning: You are using the test version of PyPI. This is a pre-production deployment of Warehouse. Changes made here affect the production instance of TestPyPI (testpypi.python.org).
Help us improve Python packaging - Donate today!

So U Found A Mutation?

Project Description

Found a mutation in one or more samples? Now you want to check if they are in another sample. Unfortunately mutect, varscan or whatever other variant caller is not calling them. Use SUFAM. The super sensitive validation caller that calls everything on a given position. All you need is a vcf with the mutations that you are interested in and the sam/bam file of the sample where you want to find the same inconsipicuous mutation.

Installation

pip install sufam

Run

usage: sufam [-h] [--sample_name SAMPLE_NAME] [--format {matrix,sufam}]
            reffa vcf bam

positional arguments:
reffa                 Reference genome (fasta)
vcf                   VCF with mutations to be validated
bam                   BAM to find mutations in

optional arguments:
-h, --help            show this help message and exit
--sample_name SAMPLE_NAME
                        Set name of sample, used in output.
--format {matrix,sufam}
                        Set output format
Release History

Release History

This version
History Node

0.1

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
sufam-0.1.linux-x86_64.tar.gz (13.5 kB) Copy SHA256 Checksum SHA256 Source Jun 16, 2015

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting