Remove HC LoF that have a likely benign or benign classification in ClinVar

[sambaxter]

Right now the pipeline is set up that all HC LoF from gnomAD variants are brought into the calculations, however I would like to modify the logic so that any HC LoF variant that has a benign or likely benign classification in ClinVar are NOT brought in.

In ticket #146 we updated the text for gnomAD variants. I would like to add a new comment to that text so its obviously that benign or likely benign variants will not be included. So the new text should state:

Include gnomAD variants based on variant type? High Confidence Loss of Function only High Confidence Loss of Function and Missense Variants with Strong REVEL score (>.932) Note: Any gnomAD variant with a likely benign or benign classification in ClinVar will NOT be included.

Methods will also need to be updated to stay (updated text is bolded): Variant List Creation The initial list of variants was created by collecting all ClinVar pathogenic and likely pathogenic variants in gnomAD for the gene and transcript specified by the user (see details above). The initial list also included any high confidence loss of function variants from gnomAD in the selected transcript that are not classified as likely benign or benign in ClinVar. High confidence loss of function variants are defined as passing QC and the transcript consequences are in the set ("stop_gained", "frameshift_variant", "splice_acceptor_variant", "splice_donor_variant", "transcript_ablation").

[sambaxter]

Adding that we should also include this logic for the High Revel scores