Liftover

Example

import gwaslab as gl

Example

gl.show_version()

stdout:

2025/12/25 22:07:57 GWASLab v4.0.0 https://cloufield.github.io/gwaslab/
2025/12/25 22:07:57 (C) 2022-2025, Yunye He, Kamatani Lab, GPL-3.0 license, gwaslab@gmail.com
2025/12/25 22:07:57 Python version: 3.12.0 | packaged by conda-forge | (main, Oct  3 2023, 08:43:22) [GCC 12.3.0]

Load sample data

Example

mysumstats = gl.Sumstats("../0_sample_data/t2d_bbj.txt.gz",
             snpid="SNP",
             chrom="CHR",
             pos="POS",
             ea="ALT",
             nea="REF",
             neaf="Frq",
             beta="BETA",
             se="SE",
             p="P",
             nrows=5000,
             verbose=False)
mysumstats.basic_check(verbose=False)

SNPID	CHR	POS	EA	NEA	STATUS	EAF	BETA	SE	P
1:725932_G_A	1	725932	G	A	9960099	0.9960	-0.0737	0.1394	0.5970
1:725933_A_G	1	725933	G	A	9960099	0.0040	0.0737	0.1394	0.5973
1:737801_T_C	1	737801	C	T	9960099	0.0051	0.0490	0.1231	0.6908
1:749963_T_TAA	1	749963	TAA	T	9960399	0.8374	0.0213	0.0199	0.2846
1:751343_T_A	1	751343	T	A	9960099	0.8593	0.0172	0.0156	0.2705
...	...	...	...	...	...	...	...	...	...
1:2150310_G_C	1	2150310	G	C	9960099	0.9913	0.0429	0.0528	0.4172
1:2150317_G_A	1	2150317	G	A	9960099	0.9930	0.1235	0.0754	0.1015
1:2150581_C_T	1	2150581	C	T	9960099	0.9981	0.1502	0.1271	0.2371
1:2151290_AAAAAC_A	1	2151290	AAAAAC	A	9960399	0.8980	0.0158	0.0152	0.2977
1:2151579_C_A	1	2151579	C	A	9960099	0.8980	0.0156	0.0152	0.3028

Example

mysumstats.data

SNPID	CHR	POS	EA	NEA	STATUS	EAF	BETA	SE	P
1:725932_G_A	1	725932	G	A	9960099	0.9960	-0.0737	0.1394	0.5970
1:725933_A_G	1	725933	G	A	9960099	0.0040	0.0737	0.1394	0.5973
1:737801_T_C	1	737801	C	T	9960099	0.0051	0.0490	0.1231	0.6908
1:749963_T_TAA	1	749963	TAA	T	9960399	0.8374	0.0213	0.0199	0.2846
1:751343_T_A	1	751343	T	A	9960099	0.8593	0.0172	0.0156	0.2705
...	...	...	...	...	...	...	...	...	...
1:2150310_G_C	1	2150310	G	C	9960099	0.9913	0.0429	0.0528	0.4172
1:2150317_G_A	1	2150317	G	A	9960099	0.9930	0.1235	0.0754	0.1015
1:2150581_C_T	1	2150581	C	T	9960099	0.9981	0.1502	0.1271	0.2371
1:2151290_AAAAAC_A	1	2151290	AAAAAC	A	9960399	0.8980	0.0158	0.0152	0.2977
1:2151579_C_A	1	2151579	C	A	9960099	0.8980	0.0156	0.0152	0.3028

[5000 rows x 10 columns]

Liftover

Example

mysumstats.liftover(from_build="19", to_build="38")

stdout:

2025/12/25 22:07:59 Start to perform liftover ...(v4.0.0)
2025/12/25 22:07:59  -Using built-in chain file: /home/yunye/anaconda3/envs/py312/lib/python3.12/site-packages/gwaslab/data/chains/hg19ToHg38.over.chain.gz
2025/12/25 22:07:59  -Converting variants with status code xxx0xxx: 5,000
2025/12/25 22:07:59  -Target build: 38
2025/12/25 22:07:59  -Input positions are 1-based
2025/12/25 22:07:59  -Output positions will be 1-based
2025/12/25 22:07:59  -Mapped: 4992 variants
2025/12/25 22:07:59  -Unmapped: 8 variants
2025/12/25 22:07:59  -Examples of unmapped variants:
2025/12/25 22:07:59    SNPID=1:1581586_T_C | CHR=1 | POS=1581586 | STATUS=9960099
2025/12/25 22:07:59    SNPID=1:1584117_G_C | CHR=1 | POS=1584117 | STATUS=9960099
2025/12/25 22:07:59    SNPID=1:1584218_T_C | CHR=1 | POS=1584218 | STATUS=9960099
2025/12/25 22:07:59    SNPID=1:1585257_A_G | CHR=1 | POS=1585257 | STATUS=9960099
2025/12/25 22:07:59    SNPID=1:1585313_CACAA_C | CHR=1 | POS=1585313 | STATUS=9960399
2025/12/25 22:07:59  -Removed 8 unmapped variants
2025/12/25 22:07:59 Start to fix chromosome notation (CHR) ...(v4.0.0)
2025/12/25 22:07:59  -Current Dataframe shape : 4992 x 10 ; Memory usage: 0.36 MB
2025/12/25 22:07:59  -Checking CHR data type...
2025/12/25 22:07:59  -Variants with standardized chromosome notation: 4992
2025/12/25 22:07:59  -All CHR are already fixed...
2025/12/25 22:07:59 Finished fixing chromosome notation (CHR).
2025/12/25 22:07:59 Start to fix basepair positions (POS) ...(v4.0.0)
2025/12/25 22:07:59  -Trying to convert datatype for POS: Int64 -> Int64...
2025/12/25 22:07:59  -Position bound:(0 , 250,000,000)
2025/12/25 22:07:59  -Removed variants outliers: 0
2025/12/25 22:07:59  -Removed variants with bad positions: 0
2025/12/25 22:07:59 Finished fixing basepair positions (POS).
2025/12/25 22:07:59 Finished liftover.

Example

mysumstats.data

SNPID	CHR	POS	EA	NEA	STATUS	EAF	BETA	SE	P
1:725932_G_A	1	790552	G	A	3860099	0.9960	-0.0737	0.1394	0.5970
1:725933_A_G	1	790553	G	A	3860099	0.0040	0.0737	0.1394	0.5973
1:737801_T_C	1	802421	C	T	3860099	0.0051	0.0490	0.1231	0.6908
1:749963_T_TAA	1	814583	TAA	T	3860399	0.8374	0.0213	0.0199	0.2846
1:751343_T_A	1	815963	T	A	3860099	0.8593	0.0172	0.0156	0.2705
...	...	...	...	...	...	...	...	...	...
1:2150310_G_C	1	2218871	G	C	3860099	0.9913	0.0429	0.0528	0.4172
1:2150317_G_A	1	2218878	G	A	3860099	0.9930	0.1235	0.0754	0.1015
1:2150581_C_T	1	2219142	C	T	3860099	0.9981	0.1502	0.1271	0.2371
1:2151290_AAAAAC_A	1	2219851	AAAAAC	A	3860399	0.8980	0.0158	0.0152	0.2977
1:2151579_C_A	1	2220140	C	A	3860099	0.8980	0.0156	0.0152	0.3028

[4992 rows x 10 columns]

Liftover using user-provided chain

Example

#https://github.com/marbl/CHM13

Example

! wget https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/grch38-chm13v2.chain

stdout:

--2025-12-25 22:08:00--  https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/grch38-chm13v2.chain
Resolving s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)... 52.92.233.24, 52.92.131.48, 52.92.233.136, ...
Connecting to s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)|52.92.233.24|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6288201 (6.0M) [binary/octet-stream]
Saving to: ‘grch38-chm13v2.chain.4’

grch38-chm13v2.chai 100%[===================>]   6.00M  3.44MB/s    in 1.7s    

2025-12-25 22:08:02 (3.44 MB/s) - ‘grch38-chm13v2.chain.4’ saved [6288201/6288201]

Example

mysumstats.data

SNPID	CHR	POS	EA	NEA	STATUS	EAF	BETA	SE	P
1:725932_G_A	1	790552	G	A	3860099	0.9960	-0.0737	0.1394	0.5970
1:725933_A_G	1	790553	G	A	3860099	0.0040	0.0737	0.1394	0.5973
1:737801_T_C	1	802421	C	T	3860099	0.0051	0.0490	0.1231	0.6908
1:749963_T_TAA	1	814583	TAA	T	3860399	0.8374	0.0213	0.0199	0.2846
1:751343_T_A	1	815963	T	A	3860099	0.8593	0.0172	0.0156	0.2705
...	...	...	...	...	...	...	...	...	...
1:2150310_G_C	1	2218871	G	C	3860099	0.9913	0.0429	0.0528	0.4172
1:2150317_G_A	1	2218878	G	A	3860099	0.9930	0.1235	0.0754	0.1015
1:2150581_C_T	1	2219142	C	T	3860099	0.9981	0.1502	0.1271	0.2371
1:2151290_AAAAAC_A	1	2219851	AAAAAC	A	3860399	0.8980	0.0158	0.0152	0.2977
1:2151579_C_A	1	2220140	C	A	3860099	0.8980	0.0156	0.0152	0.3028

[4992 rows x 10 columns]

Example

mysumstats.liftover(from_build="38", to_build="13",chain_path="./grch38-chm13v2.chain")

stdout:

2025/12/25 22:08:02 Start to perform liftover ...(v4.0.0)
2025/12/25 22:08:02  -Using provided chain file: ./grch38-chm13v2.chain
2025/12/25 22:08:02  -Converting variants with status code xxx0xxx: 4,992
2025/12/25 22:08:02  -Target build: 13
2025/12/25 22:08:02  -Input positions are 1-based
2025/12/25 22:08:02  -Output positions will be 1-based
2025/12/25 22:08:05  -Mapped: 4947 variants
2025/12/25 22:08:05  -Unmapped: 45 variants
2025/12/25 22:08:05  -Examples of unmapped variants:
2025/12/25 22:08:05    SNPID=1:844476_T_G | CHR=1 | POS=909096 | STATUS=3860099
2025/12/25 22:08:05    SNPID=1:860795_CTGCG_C | CHR=1 | POS=925415 | STATUS=3860399
2025/12/25 22:08:05    SNPID=1:871683_G_A | CHR=1 | POS=936303 | STATUS=3860099
2025/12/25 22:08:05    SNPID=1:928373_A_G | CHR=1 | POS=992993 | STATUS=3860099
2025/12/25 22:08:05    SNPID=1:930892_T_C | CHR=1 | POS=995512 | STATUS=3860099
2025/12/25 22:08:05  -Removed 45 unmapped variants
2025/12/25 22:08:05 Start to fix chromosome notation (CHR) ...(v4.0.0)
2025/12/25 22:08:05  -Current Dataframe shape : 4947 x 10 ; Memory usage: 0.36 MB
2025/12/25 22:08:05  -Checking CHR data type...
2025/12/25 22:08:05  -Variants with standardized chromosome notation: 4947
2025/12/25 22:08:05  -All CHR are already fixed...
2025/12/25 22:08:05 Finished fixing chromosome notation (CHR).
2025/12/25 22:08:05 Start to fix basepair positions (POS) ...(v4.0.0)
2025/12/25 22:08:05  -Trying to convert datatype for POS: Int64 -> Int64...
2025/12/25 22:08:05  -Position bound:(0 , 250,000,000)
2025/12/25 22:08:05  -Removed variants outliers: 0
2025/12/25 22:08:05  -Removed variants with bad positions: 0
2025/12/25 22:08:05 Finished fixing basepair positions (POS).
2025/12/25 22:08:05 Finished liftover.

Example

mysumstats.data

SNPID	CHR	POS	EA	NEA	STATUS	EAF	BETA	SE	P
1:725932_G_A	1	219468	G	A	1360099	0.9960	-0.0737	0.1394	0.5970
1:725933_A_G	1	219469	G	A	1360099	0.0040	0.0737	0.1394	0.5973
1:737801_T_C	1	231327	C	T	1360099	0.0051	0.0490	0.1231	0.6908
1:749963_T_TAA	1	243588	TAA	T	1360399	0.8374	0.0213	0.0199	0.2846
1:751343_T_A	1	244969	T	A	1360099	0.8593	0.0172	0.0156	0.2705
...	...	...	...	...	...	...	...	...	...
1:2150310_G_C	1	1654280	G	C	1360099	0.9913	0.0429	0.0528	0.4172
1:2150317_G_A	1	1654287	G	A	1360099	0.9930	0.1235	0.0754	0.1015
1:2150581_C_T	1	1654551	C	T	1360099	0.9981	0.1502	0.1271	0.2371
1:2151290_AAAAAC_A	1	1655260	AAAAAC	A	1360399	0.8980	0.0158	0.0152	0.2977
1:2151579_C_A	1	1655549	C	A	1360099	0.8980	0.0156	0.0152	0.3028

[4947 rows x 10 columns]