External sources of genetic maps

[xiangzhu]

Below are links to several genetic maps that I have used in my past work. After discussing with Peter (see Issue #3 ), it seems fine to include these external data in LDshrink as long as we properly cite these data. To make LDshrink a one-stop package for LD-related calculation, I think we should include all these files in the package (if possible).

Genetic maps listed in IMPUTE v1

• http://mathgen.stats.ox.ac.uk/impute/impute_v1.html#Using_IMPUTE_with_the_HapMap_Data
• https://mathgen.stats.ox.ac.uk/wtccc-software/recombination_rates/

Genetic maps created by Pickrell

• https://github.com/joepickrell/1000-genomes-genetic-maps

Note that these maps have very straightforward format:

$ head genetic_map_CEU_chr16.txt
position CEU_rate(cM/Mb) Genetic_Map(cM)
24045 0 0
24170 0.3020482 0
25057 0.3020482 0.0002679168
25065 0.2846052 0.0002703331
25561 0.2782453 0.0004114973
25658 0.2782453 0.0004384871
28165 0.2782453 0.001136048
29475 0.2794324 0.001500549
31010 0.2794324 0.001929478

[xiangzhu]

Both LDSC and LDAK people have included cleaned genetic maps (source unknown at this point) along with their software packages.

LDSC genetic maps

Source: https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_plinkfiles.tgz
PLINK bim format: https://www.cog-genomics.org/plink2/formats#bim

$ head -n 5 1000G.EUR.QC.9.bim
9	rs565232463	-0.054748466	12704	T	C
9	rs577055820	-0.054746525	12705	T	C
9	rs560178079	-0.052324129	13953	G	A
9	rs56270338	-0.05230666	13962	C	T
9	rs200377821	-0.050649027	14816	G	C

LDAK genetic maps

Source: http://dougspeed.com/reference-panel/

wget https://www.dropbox.com/s/slchsd0uyd4hii8/genetic_map_b37.zip?dl=0
unzip genetic_map_b37.zip

$ head -n 5 genetic_map_chr22_combined_b37.txt
position COMBINED_rate(cM/Mb) Genetic_Map(cM)
16051347 9.6640973708 0
16052618 9.7078062447 0.0123386217370137
16053624 9.7138922111 0.0221107973013803
16053659 9.716343506 0.0224508693240903