change blacklisting of variants from gene-based to region-based

[marc-sturm]

Try to come up with a region-based blacklisting of variants. Right now it's done per gene, which is wrong because only a part of a gene might be bad.

We should train a machine learning regression method to give an "artefact probability". We should train separate models for SNVs and InDels, maybe also for exome/genome.

Test with thw following variants:

• variants flagged as causal/artefact in NGSD
• de-novo variants of monozygotic twins (W:\share\evaluations\2020_07_29_twin_denovo)
• mendelian errors in trios

Test the following properties of a variant as features:

• QUAL
• DP (maybe)
• MQM
• SAP
• ABP
• In repeatmaskter region
• Distance from next repeatmasker region border

Test the following variant locus metrics as features (with different window sizes, also only left/right of variant)

• Percentage of positions with variant call in NGSD database (maybe also counts if variant calls)
• Percentage of soft-clipped reads/bases in the window
• Percentage of mismatches in the window
• Percentage of indels in the window
• Percentage/count of gnomAD variants with passing and failing quality column.
• Percentage overlap with GIAB high-confidence region of NA12878
• Percentage overlap with Platinum genomes high-confidence region of NA12877
• Percentage overlap with RepeatMasker region extended by 5 bases - also try sub-types of repeats

[marc-sturm]

Implemented low confidence regions based in gnomAD AC0/RF and in-house trio/twin regions: e7d48334cdebfd1f21ece17237b52dd8bee64652