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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.

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:

https://github.com/umich-brcf-bioinf/Zither

Quickstart

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 bfx-zither@umich.edu for support and questions.

UM BRCF Bioinformatics Core

Changelog

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

0.2

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zither-0.2.tar.gz (7.5 kB) Copy SHA256 Checksum SHA256 Source Sep 3, 2015

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