Per site nucleotide diversity

[priyanka-surana]

Description of feature

Implement the following command either using the nf-core module.

vcftools --vcf $vcf --site-pi --positions $locations --out $prefix

• Variant file is input, it can be vcf, vcf.gz or bcf
• You will need to patch in positions, it is not defined in the module. Best to combine this with bed_arg.
• positions is optional, we will most of the time not have this option

This feature requested by Alex Twyford.

[gq1]

https://vcftools.github.io/man_latest.html

--positions <filename>
--exclude-positions <filename>

Include or exclude a set of sites on the basis of a list of positions in a file.

The position file could be used as included or excluded file. Not sure what is the best way to allow user to pass the file in. Ideally, we should have 2 inputs positions_to_include and postions_to_exlcued.

This position file can be associated with site_pi flag, @priyanka-surana do you know what other flag needs this file?

How is this file related to bed_arg?

[gq1]

https://github.com/sanger-tol/variantcalling/pull/62