Handle false duplications in GRCh38

[marc-sturm]

1.3 MB of the GRCh38 reference was identified as falsely duplicated, including some medically relevant genes:
See paper https://www.nature.com/articles/s41587-021-01158-1

Masking file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_GRC_exclusions.bed

Command: bedtools/maskFastaFromBed -fi GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta -bed GCA_000001405.15_GRCh38_GRC_exclusions_T2Tv2.bed -fo GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions.fasta.

TODO:

• Add masking to genome download
• Redo analysis and compare variants (small variants, CNVs, SVs)

[marc-sturm]

Implemented in 250fb24