ContamLD dataset: Panels for estimating contamination in ancient samples

These data accompany the code: ContamLD source

Update history:
Mon Feb 3 18:11:14 EST 2020: installed, add 1240K panels

Shotgun SG_Panels:

Code Desc ChromPos
(~19Mb)
LD data
(~190Mb)
haplotype frequency data
(<207Mb)
snp frequency data
(<87Mb)
ACBAfrican Caribbeans in Barbados ACB_SG_eig_heldout_noX_ChromPos.snp.gz ACB_SG_eig_heldout_noX.ld.gz ACB_SG_haplotypefreqs_heldout_noX.txt.gz ACB_SG_snpfreqs_heldout_noX.txt.gz
ASWAmericans of African Ancestry in SW USA ASW_SG_eig_heldout_noX_ChromPos.snp.gz ASW_SG_eig_heldout_noX.ld.gz ASW_SG_haplotypefreqs_heldout_noX.txt.gz ASW_SG_snpfreqs_heldout_noX.txt.gz
BEBBengali from Bangladesh BEB_SG_eig_heldout_noX_ChromPos.snp.gz BEB_SG_eig_heldout_noX.ld.gz BEB_SG_haplotypefreqs_heldout_noX.txt.gz BEB_SG_snpfreqs_heldout_noX.txt.gz
CDXChinese Dai in Xishuangbanna, China CDX_SG_eig_heldout_noX_ChromPos.snp.gz CDX_SG_eig_heldout_noX.ld.gz CDX_SG_haplotypefreqs_heldout_noX.txt.gz CDX_SG_snpfreqs_heldout_noX.txt.gz
CEUUtah Residents (CEPH) with Northern and Western Ancestry CEU_SG_eig_heldout_noX_ChromPos.snp.gz CEU_SG_eig_heldout_noX.ld.gz CEU_SG_haplotypefreqs_heldout_noX.txt.gz CEU_SG_snpfreqs_heldout_noX.txt.gz
CHBHan Chinese in Bejing, China CHB_SG_eig_heldout_noX_ChromPos.snp.gz CHB_SG_eig_heldout_noX.ld.gz CHB_SG_haplotypefreqs_heldout_noX.txt.gz CHB_SG_snpfreqs_heldout_noX.txt.gz
CHSSouthern Han Chinese CHS_SG_eig_heldout_noX_ChromPos.snp.gz CHS_SG_eig_heldout_noX.ld.gz CHS_SG_haplotypefreqs_heldout_noX.txt.gz CHS_SG_snpfreqs_heldout_noX.txt.gz
CLMColombians from Medellin, Colombia CLM_SG_eig_heldout_noX_ChromPos.snp.gz CLM_SG_eig_heldout_noX.ld.gz CLM_SG_haplotypefreqs_heldout_noX.txt.gz CLM_SG_snpfreqs_heldout_noX.txt.gz
ESNEsan in Nigeria ESN_SG_eig_heldout_noX_ChromPos.snp.gz ESN_SG_eig_heldout_noX.ld.gz ESN_SG_haplotypefreqs_heldout_noX.txt.gz ESN_SG_snpfreqs_heldout_noX.txt.gz
FINFinnish in Finland FIN_SG_eig_heldout_noX_ChromPos.snp.gz FIN_SG_eig_heldout_noX.ld.gz FIN_SG_haplotypefreqs_heldout_noX.txt.gz FIN_SG_snpfreqs_heldout_noX.txt.gz
GBRBritish in England and Scotland GBR_SG_eig_heldout_noX_ChromPos.snp.gz GBR_SG_eig_heldout_noX.ld.gz GBR_SG_haplotypefreqs_heldout_noX.txt.gz GBR_SG_snpfreqs_heldout_noX.txt.gz
GIHGujarati Indian from Houston, Texas GIH_SG_eig_heldout_noX_ChromPos.snp.gz GIH_SG_eig_heldout_noX.ld.gz GIH_SG_haplotypefreqs_heldout_noX.txt.gz GIH_SG_snpfreqs_heldout_noX.txt.gz
GWDGambian in Western Divisions in the Gambia GWD_SG_eig_heldout_noX_ChromPos.snp.gz GWD_SG_eig_heldout_noX.ld.gz GWD_SG_haplotypefreqs_heldout_noX.txt.gz GWD_SG_snpfreqs_heldout_noX.txt.gz
IBSIberian Population in Spain IBS_SG_eig_heldout_noX_ChromPos.snp.gz IBS_SG_eig_heldout_noX.ld.gz IBS_SG_haplotypefreqs_heldout_noX.txt.gz IBS_SG_snpfreqs_heldout_noX.txt.gz
ITUIndian Telugu from the UK ITU_SG_eig_heldout_noX_ChromPos.snp.gz ITU_SG_eig_heldout_noX.ld.gz ITU_SG_haplotypefreqs_heldout_noX.txt.gz ITU_SG_snpfreqs_heldout_noX.txt.gz
JPTJapanese in Tokyo, Japan JPT_SG_eig_heldout_noX_ChromPos.snp.gz JPT_SG_eig_heldout_noX.ld.gz JPT_SG_haplotypefreqs_heldout_noX.txt.gz JPT_SG_snpfreqs_heldout_noX.txt.gz
KHVKinh in Ho Chi Minh City, Vietnam KHV_SG_eig_heldout_noX_ChromPos.snp.gz KHV_SG_eig_heldout_noX.ld.gz KHV_SG_haplotypefreqs_heldout_noX.txt.gz KHV_SG_snpfreqs_heldout_noX.txt.gz
LWKLuhya in Webuye, Kenya LWK_SG_eig_heldout_noX_ChromPos.snp.gz LWK_SG_eig_heldout_noX.ld.gz LWK_SG_haplotypefreqs_heldout_noX.txt.gz LWK_SG_snpfreqs_heldout_noX.txt.gz
MSLMende in Sierra Leone MSL_SG_eig_heldout_noX_ChromPos.snp.gz MSL_SG_eig_heldout_noX.ld.gz MSL_SG_haplotypefreqs_heldout_noX.txt.gz MSL_SG_snpfreqs_heldout_noX.txt.gz
MXLMexican Ancestry from Los Angeles USA MXL_SG_eig_heldout_noX_ChromPos.snp.gz MXL_SG_eig_heldout_noX.ld.gz MXL_SG_haplotypefreqs_heldout_noX.txt.gz MXL_SG_snpfreqs_heldout_noX.txt.gz
PELPeruvians from Lima, Peru PEL_SG_eig_heldout_noX_ChromPos.snp.gz PEL_SG_eig_heldout_noX.ld.gz PEL_SG_haplotypefreqs_heldout_noX.txt.gz PEL_SG_snpfreqs_heldout_noX.txt.gz
PJLPunjabi from Lahore, Pakistan PJL_SG_eig_heldout_noX_ChromPos.snp.gz PJL_SG_eig_heldout_noX.ld.gz PJL_SG_haplotypefreqs_heldout_noX.txt.gz PJL_SG_snpfreqs_heldout_noX.txt.gz
PURPuerto Ricans from Puerto Rico PUR_SG_eig_heldout_noX_ChromPos.snp.gz PUR_SG_eig_heldout_noX.ld.gz PUR_SG_haplotypefreqs_heldout_noX.txt.gz PUR_SG_snpfreqs_heldout_noX.txt.gz
STUSri Lankan Tamil from the UK STU_SG_eig_heldout_noX_ChromPos.snp.gz STU_SG_eig_heldout_noX.ld.gz STU_SG_haplotypefreqs_heldout_noX.txt.gz STU_SG_snpfreqs_heldout_noX.txt.gz
TSIToscani in Italia TSI_SG_eig_heldout_noX_ChromPos.snp.gz TSI_SG_eig_heldout_noX.ld.gz TSI_SG_haplotypefreqs_heldout_noX.txt.gz TSI_SG_snpfreqs_heldout_noX.txt.gz
YRIYoruba in Ibadan, Nigeria YRI_SG_eig_heldout_noX_ChromPos.snp.gz YRI_SG_eig_heldout_noX.ld.gz YRI_SG_haplotypefreqs_heldout_noX.txt.gz YRI_SG_snpfreqs_heldout_noX.txt.gz

Note: File sizes and md5sums: filesizes md5sums
All files for these SG_panels may be conveniently downloaded using the linux command: "wget -m http://reichdata.hms.harvard.edu/pub/datasets/release/contamLD/SG_panels/" (Total filesize = 13Gb).

1240K_Panels:

Code Desc ChromPos
(4Mb)
LD data
(<25Mb)
haplotype frequency data
(<37Mb)
snp frequency data
(<21Mb)
ACBAfrican Caribbeans in Barbados ACB_1240K_eig_heldout_noX_ChromPos.snp.gz ACB_1240K_eig_heldout_noX.ld.gz ACB_1240K_haplotypefreqs_heldout_noX.txt.gz ACB_1240K_snpfreqs_heldout_noX.txt.gz
ASWAmericans of African Ancestry in SW USA ASW_1240K_eig_heldout_noX_ChromPos.snp.gz ASW_1240K_eig_heldout_noX.ld.gz ASW_1240K_haplotypefreqs_heldout_noX.txt.gz ASW_1240K_snpfreqs_heldout_noX.txt.gz
BEBBengali from Bangladesh BEB_1240K_eig_heldout_noX_ChromPos.snp.gz BEB_1240K_eig_heldout_noX.ld.gz BEB_1240K_haplotypefreqs_heldout_noX.txt.gz BEB_1240K_snpfreqs_heldout_noX.txt.gz
CDXChinese Dai in Xishuangbanna, China CDX_1240K_eig_heldout_noX_ChromPos.snp.gz CDX_1240K_eig_heldout_noX.ld.gz CDX_1240K_haplotypefreqs_heldout_noX.txt.gz CDX_1240K_snpfreqs_heldout_noX.txt.gz
CEUUtah Residents (CEPH) with Northern and Western Ancestry CEU_1240K_eig_heldout_noX_ChromPos.snp.gz CEU_1240K_eig_heldout_noX.ld.gz CEU_1240K_haplotypefreqs_heldout_noX.txt.gz CEU_1240K_snpfreqs_heldout_noX.txt.gz
CHBHan Chinese in Bejing, China CHB_1240K_eig_heldout_noX_ChromPos.snp.gz CHB_1240K_eig_heldout_noX.ld.gz CHB_1240K_haplotypefreqs_heldout_noX.txt.gz CHB_1240K_snpfreqs_heldout_noX.txt.gz
CHSSouthern Han Chinese CHS_1240K_eig_heldout_noX_ChromPos.snp.gz CHS_1240K_eig_heldout_noX.ld.gz CHS_1240K_haplotypefreqs_heldout_noX.txt.gz CHS_1240K_snpfreqs_heldout_noX.txt.gz
CLMColombians from Medellin, Colombia CLM_1240K_eig_heldout_noX_ChromPos.snp.gz CLM_1240K_eig_heldout_noX.ld.gz CLM_1240K_haplotypefreqs_heldout_noX.txt.gz CLM_1240K_snpfreqs_heldout_noX.txt.gz
ESNEsan in Nigeria ESN_1240K_eig_heldout_noX_ChromPos.snp.gz ESN_1240K_eig_heldout_noX.ld.gz ESN_1240K_haplotypefreqs_heldout_noX.txt.gz ESN_1240K_snpfreqs_heldout_noX.txt.gz
FINFinnish in Finland FIN_1240K_eig_heldout_noX_ChromPos.snp.gz FIN_1240K_eig_heldout_noX.ld.gz FIN_1240K_haplotypefreqs_heldout_noX.txt.gz FIN_1240K_snpfreqs_heldout_noX.txt.gz
GBRBritish in England and Scotland GBR_1240K_eig_heldout_noX_ChromPos.snp.gz GBR_1240K_eig_heldout_noX.ld.gz GBR_1240K_haplotypefreqs_heldout_noX.txt.gz GBR_1240K_snpfreqs_heldout_noX.txt.gz
GIHGujarati Indian from Houston, Texas GIH_1240K_eig_heldout_noX_ChromPos.snp.gz GIH_1240K_eig_heldout_noX.ld.gz GIH_1240K_haplotypefreqs_heldout_noX.txt.gz GIH_1240K_snpfreqs_heldout_noX.txt.gz
GWDGambian in Western Divisions in the Gambia GWD_1240K_eig_heldout_noX_ChromPos.snp.gz GWD_1240K_eig_heldout_noX.ld.gz GWD_1240K_haplotypefreqs_heldout_noX.txt.gz GWD_1240K_snpfreqs_heldout_noX.txt.gz
IBSIberian Population in Spain IBS_1240K_eig_heldout_noX_ChromPos.snp.gz IBS_1240K_eig_heldout_noX.ld.gz IBS_1240K_haplotypefreqs_heldout_noX.txt.gz IBS_1240K_snpfreqs_heldout_noX.txt.gz
ITUIndian Telugu from the UK ITU_1240K_eig_heldout_noX_ChromPos.snp.gz ITU_1240K_eig_heldout_noX.ld.gz ITU_1240K_haplotypefreqs_heldout_noX.txt.gz ITU_1240K_snpfreqs_heldout_noX.txt.gz
JPTJapanese in Tokyo, Japan JPT_1240K_eig_heldout_noX_ChromPos.snp.gz JPT_1240K_eig_heldout_noX.ld.gz JPT_1240K_haplotypefreqs_heldout_noX.txt.gz JPT_1240K_snpfreqs_heldout_noX.txt.gz
KHVKinh in Ho Chi Minh City, Vietnam KHV_1240K_eig_heldout_noX_ChromPos.snp.gz KHV_1240K_eig_heldout_noX.ld.gz KHV_1240K_haplotypefreqs_heldout_noX.txt.gz KHV_1240K_snpfreqs_heldout_noX.txt.gz
LWKLuhya in Webuye, Kenya LWK_1240K_eig_heldout_noX_ChromPos.snp.gz LWK_1240K_eig_heldout_noX.ld.gz LWK_1240K_haplotypefreqs_heldout_noX.txt.gz LWK_1240K_snpfreqs_heldout_noX.txt.gz
MSLMende in Sierra Leone MSL_1240K_eig_heldout_noX_ChromPos.snp.gz MSL_1240K_eig_heldout_noX.ld.gz MSL_1240K_haplotypefreqs_heldout_noX.txt.gz MSL_1240K_snpfreqs_heldout_noX.txt.gz
MXLMexican Ancestry from Los Angeles USA MXL_1240K_eig_heldout_noX_ChromPos.snp.gz MXL_1240K_eig_heldout_noX.ld.gz MXL_1240K_haplotypefreqs_heldout_noX.txt.gz MXL_1240K_snpfreqs_heldout_noX.txt.gz
PELPeruvians from Lima, Peru PEL_1240K_eig_heldout_noX_ChromPos.snp.gz PEL_1240K_eig_heldout_noX.ld.gz PEL_1240K_haplotypefreqs_heldout_noX.txt.gz PEL_1240K_snpfreqs_heldout_noX.txt.gz
PJLPunjabi from Lahore, Pakistan PJL_1240K_eig_heldout_noX_ChromPos.snp.gz PJL_1240K_eig_heldout_noX.ld.gz PJL_1240K_haplotypefreqs_heldout_noX.txt.gz PJL_1240K_snpfreqs_heldout_noX.txt.gz
PURPuerto Ricans from Puerto Rico PUR_1240K_eig_heldout_noX_ChromPos.snp.gz PUR_1240K_eig_heldout_noX.ld.gz PUR_1240K_haplotypefreqs_heldout_noX.txt.gz PUR_1240K_snpfreqs_heldout_noX.txt.gz
STUSri Lankan Tamil from the UK STU_1240K_eig_heldout_noX_ChromPos.snp.gz STU_1240K_eig_heldout_noX.ld.gz STU_1240K_haplotypefreqs_heldout_noX.txt.gz STU_1240K_snpfreqs_heldout_noX.txt.gz
TSIToscani in Italia TSI_1240K_eig_heldout_noX_ChromPos.snp.gz TSI_1240K_eig_heldout_noX.ld.gz TSI_1240K_haplotypefreqs_heldout_noX.txt.gz TSI_1240K_snpfreqs_heldout_noX.txt.gz
YRIYoruba in Ibadan, Nigeria YRI_1240K_eig_heldout_noX_ChromPos.snp.gz YRI_1240K_eig_heldout_noX.ld.gz YRI_1240K_haplotypefreqs_heldout_noX.txt.gz YRI_1240K_snpfreqs_heldout_noX.txt.gz

Note: File sizes and md5sums: filesizes md5sums
All files for these 1240K_panels may be conveniently downloaded using the linux command: "wget -m http://reichdata.hms.harvard.edu/pub/datasets/release/contamLD/1240K_panels/" (Total filesize = 2.2Gb).