Here we provide some 'near production' and development versions of the code we use in our genetics research. If you have suggestions or improvements let us know.
Tools are developed according to the Small tools Manifesto principles.

1. Count_Telomeric_Sequence_Reads.py: Extracts reads containing telomeric sequences from BAM files using SAMBAMBA. Number of telomeric 6-mers that need to matched can be set. Uses multiprocessing to distribute view/count commands over different processes. Stores matching telomeric reads in a SAM file for further processing.
   Uses total read count of the SAM and BAM files to generate a normalised telomeric fraction.

1. Annotate_CADD_Scores_In_VCF.py Annotates variants in a VCF file with CADD scores using the pre-computed files provided by the University of Washington.
   Uses multiprocessing to distribute tabix lookup commands over different processes.