This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description

Command-line tool to pull raw depths and alt freqs from BAM file(s) based on an existing VCF, writing output as new VCF to stdout.

The official repository is at:


Read a single BAM file

$ zither –bam examples/explicit_bam/Sample_X.bam examples/explicit_bam/input.vcf > output.vcf

Given a VCF and a BAM file, read positions in the input VCF and corresponding pileups from Sample_X.bam.

Read a set of matched VCF sample names and BAM files

$ zither examples/matching_names/input.vcf > output.vcf

Given a VCF and a collection of BAM files whose file names match the VCF sample names, reads positions from the input VCF and corresponding BAM pileups.

Explicitly map VCF sample names to BAM files

$ zither –mapping_file=examples/mapping_files/mapping_file.txt examples/mapping_files/input.vcf > output.vcf

Given a VCF, a collection of BAMs, and a file that maps sample names to BAM paths, reads positions from the input VCF and corresponding pileups from BAM files names.

The mapping file is a tab-separated text file where each line has a sample name and the path to the corresponding BAM file. Paths to BAM files can be absolute or relative; relative paths are resolved relative to the directory that contains the mapping file.

Email for support and questions.

UM BRCF Bioinformatics Core


0.2 (9/3/2015)

  • Adjusted tags to include total and unfiltered depth and alt freq.
  • Added basecall quality filtering
  • Added depth cutoff
  • Added support for Python3

0.1 (8/6/2015)

Initial Release

Zither is written and maintained by the University of Michigan BRCF Bioinformatic Core; individual contributors include:

  • Chris Gates
  • Divya Kriti
Release History

Release History


This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
zither-0.2-py2-none-any.whl (9.4 kB) Copy SHA256 Checksum SHA256 py2 Wheel Sep 3, 2015
zither-0.2.tar.gz (7.5 kB) Copy SHA256 Checksum SHA256 Source Sep 3, 2015

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS HPE HPE Development 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