jfnavarro / hla_pipeline Goto Github PK

Replace the epitopes generation function by Varcode or improve the in-house approach to obtain
the DNA and Protein sequences from PyEnsembl instead of input files. Use only Ensembl as database
in both approaches.

Add a module and/or tool to make variant calling in HLA regions by generating
a reference in the HLA typing step and performing variant calling using this.

Adjust the percentile computation so to remove all duplicated zeroes.

Add a docker file in the repo that would make use of the latest version

It would be nice to be able to compute clonality values and add them to the
matrix with all the results.

Allow users to pass the name and path of the workdir instead of generating one in the current running directory.

Add a parameter to control how many AAs are extended from the mutation to report
epitopes (currently it is 12).

Use VEP for annotation instead of Annovar (this may make possible to remove hacks to make the VCFs compatible with Annovar)

Currently the conda version of Strelka is for Python 2

Add documentation on how to run MultiQC to obtain a nice report.
This may requires changes in the code in order to get all the information
right.

Create the testing environment and add tests for individual functions and dry runs

Use jacquard merge instead of GATK3 to merge variants (with this the awk hacks to replace IUPA REF can be removed)
Other similar tool can be used instead of jacquard merge if the behaviour is the same.