Map files are used in multiple phasing and imputation softwares.
However none of them aggree on how the file should be formated.
It can be with or without a header. All format has the physical position, the chromosome name and the corresponding cM value.
The recombination rate is optional and the column order depend on the tool.

We therefore need a tool to convert in all the different format.

Glimpse1/2 and Shapeit5 : https://github.com/odelaneau/GLIMPSE/blob/master/maps, tab separated with header: pos, chr, cumulative cM
Minimac4: https://genome.sph.umich.edu/wiki/Minimac4_Documentation, tab separated with header: chromosome id, base pair position, cumulative recombination rate in cM/Mb, and genetic map coordinates in cM (wrong format Error: target chromosome not found in genetic map file statgen/Minimac4#73), go for optional header, tabulated, chr, position, cumulative cM
Beagle5: https://faculty.washington.edu/browning/beagle/beagle_5.5_17Dec24.pdf, plink format: space separated, no header, chromosome, variant id, cumulative cM, position
Stitch & Quilt: https://github.com/rwdavies/STITCH/blob/master/STITCH.R, "3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM" position COMBINED_rate.cM.Mb. Genetic_Map.cM. (https://github.com/rwdavies/QUILT/blob/master/maps/hg38)

Stitch and quilt expect a different file for each chromosome.
We need a csv with the map file for each chromosome separated and an auto converter.

It is sometimes gziped and needs to be unzip first.

Map is not supported yet #150

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