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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.

Build Status Coverage Status

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

Project details


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This version
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0.2

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