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
