bcf-extras 0.1.0

A set of variant file helper utilities built on top of bcftools and htslib.

bcf_extras

Extra variant file helper utilities built on top of bcftools and htslib.

License

bcf_extras is licensed under GPLv3. See the license for more information.

Dependencies

The package requires that bcftools and htslib are installed on your operating system.

What's Included

copy-compress-index

Creates a .vcf.gz with a corresponding tabix index from a VCF, sorting the VCF if necessary.

For example, the following would generate sample-1.vcf.gz and sample-1.vcf.gz.tbi:

bcf-extras copy-compress-index sample-1.vcf

add-header-lines

Adds header lines from a text file to a particular position in the VCF header. Useful for e.g. inserting missing ##contig lines to a bunch of VCFs at once (taking advantage of this + something like GNU parallel.)

For the ##contig lines example, inserting the contents of tests/vcfs/new_lines.txt, we could run the following command on [tests/vcfs/ahl.vcf](tests/vcfs/ahl.vcf, replacing the file with a new copy:

bcf-extras add-header-lines tests/vcfs/ahl.vcf tests/vcfs/new_lines.txt --delete-existing

There is also a flag, --tmp-dir, for specifying a temporary folder location into which header artifacts will be placed. This is especially useful when running jobs on clusters, which may have specific locations for temporary I/O.

Using GNU parallel, we can do multiple VCFs at once, e.g.:

parallel 'bcf-extras add-header-lines {} tests/vcfs/new_lines.txt --delete-existing' ::: /path/to/my/vcfs/*.vcf