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:
$ 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.
$ 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.
$ 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 firstname.lastname@example.org for support and questions.
UM BRCF Bioinformatics Core
Zither is written and maintained by the University of Michigan BRCF Bioinformatic Core; individual contributors include:
TODO: Figure out how to actually get changelog content.
Changelog content for this version goes here.
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|