Liftover¶

In [1]:

import gwaslab as gl

import gwaslab as gl

In [2]:

gl.show_version()

gl.show_version()

2024/12/21 18:01:36 GWASLab v3.5.4 https://cloufield.github.io/gwaslab/
2024/12/21 18:01:36 (C) 2022-2024, Yunye He, Kamatani Lab, MIT License, gwaslab@gmail.com

Load sample data¶

In [3]:

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)

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)

In [4]:

mysumstats.data

mysumstats.data

Out[4]:

	SNPID	CHR	POS	EA	NEA	EAF	BETA	SE	P	STATUS
0	1:725932_G_A	1	725932	G	A	0.9960	-0.0737	0.1394	0.5970	9960099
1	1:725933_A_G	1	725933	G	A	0.0040	0.0737	0.1394	0.5973	9960099
2	1:737801_T_C	1	737801	C	T	0.0051	0.0490	0.1231	0.6908	9960099
3	1:749963_T_TAA	1	749963	TAA	T	0.8374	0.0213	0.0199	0.2846	9960399
4	1:751343_T_A	1	751343	T	A	0.8593	0.0172	0.0156	0.2705	9960099
...	...	...	...	...	...	...	...	...	...	...
4995	1:2150310_G_C	1	2150310	G	C	0.9913	0.0429	0.0528	0.4172	9960099
4996	1:2150317_G_A	1	2150317	G	A	0.9930	0.1235	0.0754	0.1015	9960099
4997	1:2150581_C_T	1	2150581	C	T	0.9981	0.1502	0.1271	0.2371	9960099
4998	1:2151290_AAAAAC_A	1	2151290	AAAAAC	A	0.8980	0.0158	0.0152	0.2977	9960399
4999	1:2151579_C_A	1	2151579	C	A	0.8980	0.0156	0.0152	0.3028	9960099

5000 rows × 10 columns

Liftover¶

In [5]:

mysumstats.liftover(n_cores=3, from_build="19", to_build="38")

mysumstats.liftover(n_cores=3, from_build="19", to_build="38")

2024/12/21 18:01:50 Start to perform liftover...v3.5.4
2024/12/21 18:01:50  -Current Dataframe shape : 5000 x 10 ; Memory usage: 21.77 MB
2024/12/21 18:01:50  -Number of threads/cores to use: 3
2024/12/21 18:01:50  -Creating converter using provided ChainFile: /home/yunye/.gwaslab/hg19ToHg38.over.chain.gz
2024/12/21 18:01:50  -Creating converter : 19 -> 38
2024/12/21 18:01:51  -Converting variants with status code xxx0xxx :5000...
2024/12/21 18:01:52  -Removed unmapped variants: 2
2024/12/21 18:01:52 Start to fix chromosome notation (CHR)...v3.5.4
2024/12/21 18:01:52  -Current Dataframe shape : 4998 x 10 ; Memory usage: 0.36 MB
2024/12/21 18:01:52  -Checking CHR data type...
2024/12/21 18:01:52  -Variants with standardized chromosome notation: 4998
2024/12/21 18:01:52  -All CHR are already fixed...
2024/12/21 18:01:53 Finished fixing chromosome notation (CHR).
2024/12/21 18:01:53 Start to fix basepair positions (POS)...v3.5.4
2024/12/21 18:01:53  -Current Dataframe shape : 4998 x 10 ; Memory usage: 21.81 MB
2024/12/21 18:01:53  -Removing thousands separator "," or underbar "_" ...
2024/12/21 18:01:53  -Converting to Int64 data type ...
2024/12/21 18:01:56  -Position bound:(0 , 250,000,000)
2024/12/21 18:01:56  -Removed outliers: 0
2024/12/21 18:01:56  -Removed 0 variants with bad positions.
2024/12/21 18:01:56 Finished fixing basepair positions (POS).
2024/12/21 18:01:56 Finished liftover.

In [6]:

mysumstats.data

mysumstats.data

Out[6]:

	SNPID	CHR	POS	EA	NEA	EAF	BETA	SE	P	STATUS
0	1:725932_G_A	1	790552	G	A	0.9960	-0.0737	0.1394	0.5970	3860099
1	1:725933_A_G	1	790553	G	A	0.0040	0.0737	0.1394	0.5973	3860099
2	1:737801_T_C	1	802421	C	T	0.0051	0.0490	0.1231	0.6908	3860099
3	1:749963_T_TAA	1	814583	TAA	T	0.8374	0.0213	0.0199	0.2846	3860399
4	1:751343_T_A	1	815963	T	A	0.8593	0.0172	0.0156	0.2705	3860099
...	...	...	...	...	...	...	...	...	...	...
4995	1:2150310_G_C	1	2218871	G	C	0.9913	0.0429	0.0528	0.4172	3860099
4996	1:2150317_G_A	1	2218878	G	A	0.9930	0.1235	0.0754	0.1015	3860099
4997	1:2150581_C_T	1	2219142	C	T	0.9981	0.1502	0.1271	0.2371	3860099
4998	1:2151290_AAAAAC_A	1	2219851	AAAAAC	A	0.8980	0.0158	0.0152	0.2977	3860399
4999	1:2151579_C_A	1	2220140	C	A	0.8980	0.0156	0.0152	0.3028	3860099

4998 rows × 10 columns

Liftover using user-provided chain¶

In [7]:

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

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

In [8]:

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

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

--2024-12-21 18:01:56--  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)... 52.92.228.232, 3.5.76.241, 52.218.216.160, ...
Connecting to s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)|52.92.228.232|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6288201 (6.0M) [binary/octet-stream]
Saving to: ‘grch38-chm13v2.chain.1’

grch38-chm13v2.chai 100%[===================>]   6.00M  2.01MB/s    in 3.0s    

2024-12-21 18:02:00 (2.01 MB/s) - ‘grch38-chm13v2.chain.1’ saved [6288201/6288201]

In [9]:

mysumstats.data

mysumstats.data

Out[9]:

	SNPID	CHR	POS	EA	NEA	EAF	BETA	SE	P	STATUS
0	1:725932_G_A	1	790552	G	A	0.9960	-0.0737	0.1394	0.5970	3860099
1	1:725933_A_G	1	790553	G	A	0.0040	0.0737	0.1394	0.5973	3860099
2	1:737801_T_C	1	802421	C	T	0.0051	0.0490	0.1231	0.6908	3860099
3	1:749963_T_TAA	1	814583	TAA	T	0.8374	0.0213	0.0199	0.2846	3860399
4	1:751343_T_A	1	815963	T	A	0.8593	0.0172	0.0156	0.2705	3860099
...	...	...	...	...	...	...	...	...	...	...
4995	1:2150310_G_C	1	2218871	G	C	0.9913	0.0429	0.0528	0.4172	3860099
4996	1:2150317_G_A	1	2218878	G	A	0.9930	0.1235	0.0754	0.1015	3860099
4997	1:2150581_C_T	1	2219142	C	T	0.9981	0.1502	0.1271	0.2371	3860099
4998	1:2151290_AAAAAC_A	1	2219851	AAAAAC	A	0.8980	0.0158	0.0152	0.2977	3860399
4999	1:2151579_C_A	1	2220140	C	A	0.8980	0.0156	0.0152	0.3028	3860099

4998 rows × 10 columns

In [10]:

mysumstats.liftover(n_cores=1, from_build="38", to_build="13",chain="./grch38-chm13v2.chain")

mysumstats.liftover(n_cores=1, from_build="38", to_build="13",chain="./grch38-chm13v2.chain")

2024/12/21 18:02:00 Start to perform liftover...v3.5.4
2024/12/21 18:02:00  -Current Dataframe shape : 4998 x 10 ; Memory usage: 21.81 MB
2024/12/21 18:02:00  -Number of threads/cores to use: 1
2024/12/21 18:02:00  -Creating converter using ChainFile: ./grch38-chm13v2.chain
2024/12/21 18:02:00  -Creating converter : 38 -> 13
2024/12/21 18:02:01  -Converting variants with status code xxx0xxx :4998...
2024/12/21 18:02:03  -Removed unmapped variants: 44
2024/12/21 18:02:03 Start to fix chromosome notation (CHR)...v3.5.4
2024/12/21 18:02:03  -Current Dataframe shape : 4954 x 10 ; Memory usage: 0.36 MB
2024/12/21 18:02:03  -Checking CHR data type...
2024/12/21 18:02:03  -Variants with standardized chromosome notation: 4954
2024/12/21 18:02:03  -All CHR are already fixed...
2024/12/21 18:02:04 Finished fixing chromosome notation (CHR).
2024/12/21 18:02:04 Start to fix basepair positions (POS)...v3.5.4
2024/12/21 18:02:04  -Current Dataframe shape : 4954 x 10 ; Memory usage: 21.80 MB
2024/12/21 18:02:04  -Removing thousands separator "," or underbar "_" ...
2024/12/21 18:02:04  -Converting to Int64 data type ...
2024/12/21 18:02:07  -Position bound:(0 , 250,000,000)
2024/12/21 18:02:07  -Removed outliers: 0
2024/12/21 18:02:07  -Removed 0 variants with bad positions.
2024/12/21 18:02:07 Finished fixing basepair positions (POS).
2024/12/21 18:02:07 Finished liftover.

In [11]:

mysumstats.data

mysumstats.data

Out[11]:

	SNPID	CHR	POS	EA	NEA	EAF	BETA	SE	P	STATUS
0	1:725932_G_A	1	219468	G	A	0.9960	-0.0737	0.1394	0.5970	1360099
1	1:725933_A_G	1	219469	G	A	0.0040	0.0737	0.1394	0.5973	1360099
2	1:737801_T_C	1	231327	C	T	0.0051	0.0490	0.1231	0.6908	1360099
3	1:749963_T_TAA	1	243588	TAA	T	0.8374	0.0213	0.0199	0.2846	1360399
4	1:751343_T_A	1	244969	T	A	0.8593	0.0172	0.0156	0.2705	1360099
...	...	...	...	...	...	...	...	...	...	...
4995	1:2150310_G_C	1	1654280	G	C	0.9913	0.0429	0.0528	0.4172	1360099
4996	1:2150317_G_A	1	1654287	G	A	0.9930	0.1235	0.0754	0.1015	1360099
4997	1:2150581_C_T	1	1654551	C	T	0.9981	0.1502	0.1271	0.2371	1360099
4998	1:2151290_AAAAAC_A	1	1655260	AAAAAC	A	0.8980	0.0158	0.0152	0.2977	1360399
4999	1:2151579_C_A	1	1655549	C	A	0.8980	0.0156	0.0152	0.3028	1360099

4954 rows × 10 columns