Create C4R repeat expansion database

[Madelinehazel]

We use TRGT to call short repeat expansions from PacBio HiFi genomes. We would like to develop a 'database' that tells us the minimum and maximum repeat size we've seen in our samples for each repeat locus.

This will be a text file that contains the minimum and maximum repeat size for each repeat, as well as sample names corresponding to those carrying the minimum and maximum allele sizes. Example line:

repeat	min_size	max_size	min_size_sample	max_size_sample
chr10_100000834_100000912_A	50	80	HG00639	HG00099

You may generate this from HPRC (human pangenome reference consortium) and C4R TRGT VCFs in: /hpf/largeprojects/ccmbio/ccmmarvin_shared/pacbio_longread/TRGT/proband_only_workflow/HPRC-C4R-VCFs. OR, generate from this text file: /hpf/largeprojects/ccmbio/mcouse/pacbio_report_dev/results/test_outlier_expansions_full/repeat_outliers/sorted_alleles_db.gz, which was derived from the HPRC and C4R VCFs (probably easiest to start here)

See section 'Find outliers' in this notebook for possible inspiration on how to iterate through/handle the file.

Note: HPRC TRGT VCFs came from Egor. We do not have HPRC BAMs on the hpf.