This folder contains resources used to make hitplots in the GWAS practical.

The file refGene_chr19.txt, containing RefSeq gene annotations, is an extract from the
UCSC Genome Browser 'refGene table'.  You can get this from the 'table browser'
at https://genome.ucsc.edu/cgi-bin/hgTables

The file snp138_chr19.txt.gz is likewise extracted from the UCSC Genome Browser
snp138 table, also available from the table browser.  (Note that a download of the
full table is very large.)

(Another way to access the above data is using the UCSC Genome Browser public
MySQL instance.  See https://genome.ucsc.edu/goldenPath/help/mysql.html
for more information.)

The file genetic_map_chr19_combined_b37.txt was obtained as part of the 1000
Genome reference panel made available on the IMPUTE website:
https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference.
It can also be downloaded from the SHAPEIT website:
https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#gmap

(At the time of writing, most studies work in build 37 coordinates, although
the latest genome assembly is build 38.)