semvec/pypi-packages huggingface dataset:
zither 0.2
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.
License: Apache
Keywords: VCF bioinformatic exome-seq DNA-seq variant-call-format BAM

====== 
Zither
======

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.

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The official repository is at:

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

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Quickstart
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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