LiftOver - Revision history

Zhanxw: /* Resources */

2015-07-15T22:33:41Z

Resources

← Older revision		Revision as of 18:33, 15 July 2015
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	== Resources ==		== Resources ==
	* liftRsNumber.py [[liftRsNumber.py]] and its interal location: /net/~~dumbo/net/dumbo~~/home/zhanxw/amd/analyze/verifyBamID/liftRsNumber.py		* liftRsNumber.py [[liftRsNumber.py]] and its interal location: /net/fantasia/home/zhanxw/amd/analyze/verifyBamID/liftRsNumber.py
	* liftMap.py [[liftMap.py]]		* liftMap.py [[liftMap.py]]
	* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]		* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]
	* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]		* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]
	* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]		* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]
	* NCBI SNPChrPosOnRef build 132 [~~ftp~~://~~ftp~~.~~ncbi~~.~~nih.gov:~~/~~snp~~/~~organisms/human_9606/database/b132_archive~~/~~organism_data~~/b132_SNPChrPosOnRef_37_1.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPChrPosOnRef schema]. If this link becomes unavailable, please consider using ~~the~~ updated file ([ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/~~b141_SNPChrPosOnRef~~.bcp.gz link]).		* NCBI SNPChrPosOnRef build 132 [http://qbrc.swmed.edu/zhanxw/software/liftOver/b132_SNPChrPosOnRef_37_1.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPChrPosOnRef schema]. If this link becomes unavailable, please consider using this updated file ([ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/b144_SNPChrPosOnRef_107.bcp.gz link]).

	* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]		* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]

Zhanxw: /* Resources */

2014-10-14T05:40:36Z

Resources

← Older revision		Revision as of 01:40, 14 October 2014
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	* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]		* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]
	* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]		* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]
	* NCBI SNPChrPosOnRef build 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/b132_archive/organism_data/b132_SNPChrPosOnRef_37_1.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPChrPosOnRef schema]		* NCBI SNPChrPosOnRef build 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/b132_archive/organism_data/b132_SNPChrPosOnRef_37_1.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPChrPosOnRef schema]. If this link becomes unavailable, please consider using the updated file ([ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/b141_SNPChrPosOnRef.bcp.gz link]).

	* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]		* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]
	* The dbSNP mapping process [http://www.ncbi.nlm.nih.gov/books/NBK44455/ link]		* The dbSNP mapping process [http://www.ncbi.nlm.nih.gov/books/NBK44455/ link]
	* NCBI dbSNP release 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz 00-All.vcf.gz]		* NCBI dbSNP release 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz 00-All.vcf.gz]
	* UCSC dbSNP release 132 [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz snp132.txt.gz]		* UCSC dbSNP release 132 [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz snp132.txt.gz]


	== Third party contribution ==		== Third party contribution ==

Zhanxw: /* Resources */

2014-02-14T15:12:53Z

Resources

← Older revision		Revision as of 11:12, 14 February 2014
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	* NCBI dbSNP release 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz 00-All.vcf.gz]		* NCBI dbSNP release 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz 00-All.vcf.gz]
	* UCSC dbSNP release 132 [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz snp132.txt.gz]		* UCSC dbSNP release 132 [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz snp132.txt.gz]


			== Third party contribution ==

			* liftOver for BEDPE format by [mailto://doug.phanstiel@gmail.com Doug] - [http://www.sharedproteomics.com/forum/showthread.php?2930-liftOverBedpe.py-Convert-genome-coordinates-for-bedpe-files&p=4854#post4854 liftOverBedpe.py].

	== Acknowledge ==		== Acknowledge ==

Zhanxw: /* Use RsMergeArch and SNPHistory */

2012-06-18T23:47:45Z

Use RsMergeArch and SNPHistory

← Older revision		Revision as of 19:47, 18 June 2012
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	Example input:		Example input:
	<pre>		<pre>
	~~3115860~~		3000
	~~12124819~~		3001
	~~2229002~~		3002
	~~1130683~~
	</pre>		</pre>

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	</pre>		</pre>

	Example ~~otuput~~:		Example output:
	<pre>		<pre>
	unchanged ~~3115860~~		unchanged 3000
	~~unchanged 12124819~~		lifted 2032
	lifted ~~2229002~~		unchanged 3002
	~~lifted 1130683~~
	</pre>		</pre>

Zhanxw at 20:27, 27 September 2011

2011-09-27T20:27:09Z

← Older revision		Revision as of 16:27, 27 September 2011
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	With the above in mind, we are able to combine these two tables to obtain the relationship between older rs number and new rs number.		With the above in mind, we are able to combine these two tables to obtain the relationship between older rs number and new rs number.
	We have developed a script (for internal use), named [http://genome.sph.umich.edu/wiki/LiftRsNumber.py liftRsNumber.py] ~~AAAA~~ for lift rs numbers between builds.		We have developed a script (for internal use), named [http://genome.sph.umich.edu/wiki/LiftRsNumber.py liftRsNumber.py] for lift rs numbers between builds.
	This scripts require RsMergeArch.bcp.gz and SNPHistory.bcp.gz, those can be found in [[#Resources \| Resources]].		This scripts require RsMergeArch.bcp.gz and SNPHistory.bcp.gz, those can be found in [[#Resources \| Resources]].

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	Similar to the human reference build, dbSNP also have different versions. You may consider change rs number from the old dbSNP version to new dbSNP version		Similar to the human reference build, dbSNP also have different versions. You may consider change rs number from the old dbSNP version to new dbSNP version
	depending on your needs. Such steps are described in [[#Lift dbSNP rs numbers \| Lift dbSNP rs numbers]]. ~~AAAA~~		depending on your needs. Such steps are described in [[#Lift dbSNP rs numbers \| Lift dbSNP rs numbers]].

	==== Method 2 ====		==== Method 2 ====
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	(2) Lookup SNP positions from rs number		(2) Lookup SNP positions from rs number

	dbSNP provides a file [[#Resources \| ~~joinb132_SNPChrPosOnRef_37_1~~.bcp.gz]] which contains rsNumber, chromosome and its position.		dbSNP provides a file [[#Resources \| b132_SNPChrPosOnRef_37_1.bcp.gz]] which contains rsNumber, chromosome and its position.
	Use this file along with the new rsNumber obtained in the first step.		Use this file along with the new rsNumber obtained in the first step.
	In practice, some rs numbers do not exist in build 132, or not suitable to be considered ( e.g. they do not reside on human reference, or they are mapped to multiple locations, these scenarios are noted by the chromosome column with values like "AltOnly", "Multi", "NotOn", "PAR", "Un"), we can drop them in the liftover procedure.		In practice, some rs numbers do not exist in build 132, or not suitable to be considered ( e.g. they do not reside on human reference, or they are mapped to multiple locations, these scenarios are noted by the chromosome column with values like "AltOnly", "Multi", "NotOn", "PAR", "Un"), we can drop them in the liftover procedure.
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	==== Method 3 ====		==== Method 3 ====
	NCBI dbSNP team has provided a [[ #Resources \| provisional map ]] ~~AAAA~~ for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.		NCBI dbSNP team has provided a [[ #Resources \| provisional map ]] for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.
	In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.		In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.
	After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.		After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.
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	Please contact [mailto:zhanxw@umich.edu Xiaowei Zhan].		Please contact [mailto:zhanxw@umich.edu Xiaowei Zhan].


	~~AAAA~~

Zhanxw at 03:39, 24 September 2011

2011-09-24T03:39:17Z

← Older revision		Revision as of 23:39, 23 September 2011
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	LiftOver can have three use cases:		LiftOver can have three use cases:

	(1) [[#Lift genome positions \| ~~convert~~ genome position from one genome assembly to another genome assembly]]		(1) [[#Lift genome positions \| Convert genome position from one genome assembly to another genome assembly]]

	In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).		In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

	(2) [[#Lift dbSNP rs numbers \| ~~convert~~ dbSNP rs number from one build to another]]		(2) [[#Lift dbSNP rs numbers \| Convert dbSNP rs number from one build to another]]

			(3) [[#Lift Merlin/PLINK format \| Convert both genome position and dbSNP rs number over different versions]]

	~~(3) [[#Lift Merlin/PLINK format \|convert both genome position and dbSNP rs number over different versions]]~~
	It is likely to see such type of data in Merlin/PLINK format.		It is likely to see such type of data in Merlin/PLINK format.

Zhanxw at 03:37, 24 September 2011

2011-09-24T03:37:11Z

← Older revision		Revision as of 23:37, 23 September 2011
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	With the above in mind, we are able to combine these two tables to obtain the relationship between older rs number and new rs number.		With the above in mind, we are able to combine these two tables to obtain the relationship between older rs number and new rs number.
	We have developed a script (for internal use), named ~~liftRsNumber.py~~ [/~~net~~ /~~dumbo~~/~~net/dumbo/home/zhanxw/amd/analyze/verifyBamID~~/] for lift rs numbers between builds.		We have developed a script (for internal use), named [http://genome.sph.umich.edu/wiki/LiftRsNumber.py liftRsNumber.py] AAAA for lift rs numbers between builds.
	This scripts require RsMergeArch.bcp.gz and SNPHistory.bcp.gz, those can be found in [[#Resources \| Resources]].		This scripts require RsMergeArch.bcp.gz and SNPHistory.bcp.gz, those can be found in [[#Resources \| Resources]].

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	== Lift Merlin/PLINK format ==		== Lift Merlin/PLINK format ==
	In Merlin/PLINK .map files, each line contains both genome position and dbSNP rs number. Our goal here is to use both information to liftOver as many position as possible.		In Merlin/PLINK .map files, each line contains both genome position and dbSNP rs number. Our goal here is to use both information to liftOver as many position as possible.
	There are 3 methods to liftOver and we recommend the first 2 method. The first method is common, and it lifts most genome positions, however, it does not reflect the dbSNP ~~build change~~. The second method is more robust in the sense that each lifted rs number has valid genome position, as ~~its uses~~ dbSNP as data ~~source~~. The third method is not straigtforward, and we just briefly mention it.		There are 3 methods to liftOver and we recommend the first 2 method. The first method is common and applicable in most cases, and in our observations it lifts the most genome positions, however, it does not reflect the rs number change between different dbSNP builds. The second method is more robust in the sense that each lifted rs number has valid genome position, as it lift over old rs number as the first step by using dbSNP data. The third method is not straigtforward, and we just briefly mention it.

	=== Lift Merlin format ===		=== Lift Merlin format ===
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	Similar to the human reference build, dbSNP also have different versions. You may consider change rs number from the old dbSNP version to new dbSNP version		Similar to the human reference build, dbSNP also have different versions. You may consider change rs number from the old dbSNP version to new dbSNP version
	depending on your needs Such steps are described in [#Lift dbSNP rs numbers \| Lift dbSNP rs numbers].		depending on your needs. Such steps are described in [[#Lift dbSNP rs numbers \| Lift dbSNP rs numbers]]. AAAA

	==== Method 2 ====		==== Method 2 ====
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	==== Method 3 ====		==== Method 3 ====
	NCBI dbSNP team has provided a [#Resources \| provisional map] for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.		NCBI dbSNP team has provided a [[ #Resources \| provisional map ]] AAAA for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.
	In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.		In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.
	After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.		After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.
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	Accordingly, we need to deleted SNP genotypes for those cannot be lifted.		Accordingly, we need to deleted SNP genotypes for those cannot be lifted.

	== Various reasons that lift over ~~could~~ fail ==		== Various reasons that lift over can fail ==

	=== Genome position cannot be lifted ===		=== Genome position cannot be lifted ===
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	It is possible that new dbSNP build does not have certain rs numbers.		It is possible that new dbSNP build does not have certain rs numbers.
	When dbSNp release new build, higher rs number may be merged to lower rs number because of those rs numbers are actually the same SNP.		When dbSNp release new build, higher rs number may be merged to lower rs number because of those rs numbers are actually the same SNP.
	This merge process can be complicate. For short description, see [#Use RsMergeArch and SNPHistory \| Use RsMergeArch and SNPHistory].		This merge process can be complicate. For short description, see [[ #Use RsMergeArch and SNPHistory \| Use RsMergeArch and SNPHistory ]].
	For detail, see:		For detail, see:

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	* SNPs that are not mapped on the reference genome (GRCh37)		* SNPs that are not mapped on the reference genome (GRCh37)

	For UCSC release, see [#Resources \| UCSC dbSNP track note]		For UCSC release, see [[ #Resources \| UCSC dbSNP track note ]]

	Use rs1054140 as an example:		Use rs1054140 as an example:
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	== Resources ==		== Resources ==
	* liftRsNumber.py [[liftRsNumber.py]]		* liftRsNumber.py [[liftRsNumber.py]] and its interal location: /net/dumbo/net/dumbo/home/zhanxw/amd/analyze/verifyBamID/liftRsNumber.py
	* liftMap.py [[liftMap.py]]		* liftMap.py [[liftMap.py]]
	* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]		* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]
	* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]		* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]
	* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]		* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]
			* NCBI SNPChrPosOnRef build 132 [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/b132_archive/organism_data/b132_SNPChrPosOnRef_37_1.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPChrPosOnRef schema]
	* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]		* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]
	* The dbSNP mapping process [http://www.ncbi.nlm.nih.gov/books/NBK44455/ link]		* The dbSNP mapping process [http://www.ncbi.nlm.nih.gov/books/NBK44455/ link]
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	Please contact [mailto:zhanxw@umich.edu Xiaowei Zhan].		Please contact [mailto:zhanxw@umich.edu Xiaowei Zhan].


			AAAA

Zhanxw: /* Resources */

2011-08-10T15:34:35Z

Resources

← Older revision		Revision as of 11:34, 10 August 2011
Line 234:		Line 234:

	== Resources ==		== Resources ==
	* liftRsNumber.py []		* liftRsNumber.py [[liftRsNumber.py]]
	* liftMap.py []		* liftMap.py [[liftMap.py]]
	* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]		* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]
	* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]		* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]

Zhanxw at 15:24, 10 August 2011

2011-08-10T15:24:05Z

Zhanxw at 15:23, 10 August 2011

2011-08-10T15:23:52Z

Show changes

← Older revision		Revision as of 11:24, 10 August 2011
Line 2:		Line 2:
	LiftOver can have three use cases:		LiftOver can have three use cases:

	(1) [[#Lift ~~genomic~~ positions \| convert ~~genomic~~ position from one genome assembly to another genome assembly]]		(1) [[#Lift genome positions \| convert genome position from one genome assembly to another genome assembly]]
	In most scenarios, we have known ~~genomic~~ positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).		In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

	(2) [[#Lift dbSNP rs numbers \| convert dbSNP rs number from one build to another]]		(2) [[#Lift dbSNP rs numbers \| convert dbSNP rs number from one build to another]]

	(3) [[#Lift Merlin/PLINK format \|convert both ~~genomic~~ position and dbSNP rs number over different versions]]		(3) [[#Lift Merlin/PLINK format \|convert both genome position and dbSNP rs number over different versions]]
	It is likely to see such type of data in Merlin/PLINK format.		It is likely to see such type of data in Merlin/PLINK format.

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	With our customized scripts, we can also lift rsNumber and Merlin/PLINK data files.		With our customized scripts, we can also lift rsNumber and Merlin/PLINK data files.

	== Lift ~~genomic~~ positions ==		== Lift genome positions ==
	~~Genomic~~ positions are best represented in [http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format]. UCSC provides tools to convert BED file from one genome assembly to another.		Genome positions are best represented in [http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED format]. UCSC provides tools to convert BED file from one genome assembly to another.

	=== Binary liftOver tool ===		=== Binary liftOver tool ===
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	liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed		liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed

	unlifted.bed file will contain all ~~genomic~~ positions that cannot be lifted. The reason for that varies. See [[#Various reasons that lift over could fail \| Various reasons that lift over could fail]]		unlifted.bed file will contain all genome positions that cannot be lifted. The reason for that varies. See [[#Various reasons that lift over could fail \| Various reasons that lift over could fail]]

	=== Web interface ===		=== Web interface ===
	Alternatively, you can lift over BED file in web interface		Alternatively, you can lift over BED file in web interface
	at: [http://genome.ucsc.edu/cgi-bin/hgLiftOver Link]		at: [http://genome.ucsc.edu/cgi-bin/hgLiftOver Link]
	Web interface can tell you why some ~~genomic~~ position cannot		Web interface can tell you why some genome position cannot
	be lifted if you click "Explain failure messages"		be lifted if you click "Explain failure messages"

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	== Lift Merlin/PLINK format ==		== Lift Merlin/PLINK format ==
	In Merlin/PLINK .map files, each line contains both ~~genomic~~ position and dbSNP rs number. Our goal here is to use both information to liftOver as many position as possible.		In Merlin/PLINK .map files, each line contains both genome position and dbSNP rs number. Our goal here is to use both information to liftOver as many position as possible.
	There are 3 methods to liftOver and we recommend the first 2 method. The first method is common, and it lifts most ~~genomic~~ positions, however, it does not reflect the dbSNP build change. The second method is more robust in the sense that each lifted rs number has valid ~~genomic~~ position, as its uses dbSNP as data source. The third method is not straigtforward, and we just briefly mention it.		There are 3 methods to liftOver and we recommend the first 2 method. The first method is common, and it lifts most genome positions, however, it does not reflect the dbSNP build change. The second method is more robust in the sense that each lifted rs number has valid genome position, as its uses dbSNP as data source. The third method is not straigtforward, and we just briefly mention it.

	=== Lift Merlin format ===		=== Lift Merlin format ===
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	(2) LiftOver .bed file		(2) LiftOver .bed file

	Use method mentioned [[#Lift ~~genomic~~ positions \| above]] to convert .bed file from one build to another.		Use method mentioned [[#Lift genome positions \| above]] to convert .bed file from one build to another.

	(3) Convert lifted .bed file back to .map file		(3) Convert lifted .bed file back to .map file
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	.ped file have many column files. By convention, the first six columns are family_id, person_id, father_id, mother_id, sex, and phenotype.		.ped file have many column files. By convention, the first six columns are family_id, person_id, father_id, mother_id, sex, and phenotype.
	From the 7th column, there are two letters/digits representing a genotype at the certain marker. In step (2), as some ~~genomic~~ positions cannot		From the 7th column, there are two letters/digits representing a genotype at the certain marker. In step (2), as some genome positions cannot
	be lifted to the new version, we need to drop their corresponding columns from .ped file to keep consistency. You can use PLINK --exclude those snps,		be lifted to the new version, we need to drop their corresponding columns from .ped file to keep consistency. You can use PLINK --exclude those snps,
	see [http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#exclude Remove a subset of SNPs].		see [http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#exclude Remove a subset of SNPs].
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	==== Method 3 ====		==== Method 3 ====
	NCBI dbSNP team has provided a [#Resources \| provisional map] for converting the ~~genomic~~ position of a larget set dbSNP from NCBI build 36 to NCBI build 37.		NCBI dbSNP team has provided a [#Resources \| provisional map] for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.
	In the second step, we have obtained unlifted ~~genomic~~ positions, so we can try to use the table to convert those unlfted dbSNPs.		In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.
	After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.		After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.
	Note: due to the limitation of the provisional map, some SNP can have multiple locations.		Note: due to the limitation of the provisional map, some SNP can have multiple locations.
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	(2) Use provisional map to update .map file		(2) Use provisional map to update .map file

	By joining .map file and this provisional map, we can obtain the new ~~genomic~~ position in the new build.		By joining .map file and this provisional map, we can obtain the new genome position in the new build.
	Note: provisional map uses 1-based chromosomal index. Things will get tricker if we want to lift non-single site SNP e.g. AA/GG		Note: provisional map uses 1-based chromosomal index. Things will get tricker if we want to lift non-single site SNP e.g. AA/GG
	Since provisional map provides a range in this case, it is necessary to know the ~~genomic~~ position of that single base provided in the .map file,		Since provisional map provides a range in this case, it is necessary to know the genome position of that single base provided in the .map file,
	and then we can look up the table, so it is not straigtforward.		and then we can look up the table, so it is not straigtforward.

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	== Various reasons that lift over could fail ==		== Various reasons that lift over could fail ==

	=== ~~Genomic~~ position cannot be lifted ===		=== Genome position cannot be lifted ===
	When a SNP resides in a contig that only exists in older reference build, liftOver cannot give it new ~~genomic~~.		When a SNP resides in a contig that only exists in older reference build, liftOver cannot give it new genome.

	You can try the following SNP (in BED format) in UCSC online liftOver site:		You can try the following SNP (in BED format) in UCSC online liftOver site:
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	=== SNP in higher build are located in non-referernce assembly ===		=== SNP in higher build are located in non-referernce assembly ===
	Some SNP are not in autosomes or sex chromosomes in NCBI build 37. dbSNP does not include them.		Some SNP are not in autosomes or sex chromosomes in NCBI build 37. dbSNP does not include them.
	You cannot use dbSNP database to lookup its ~~genomic~~ position by rs number.		You cannot use dbSNP database to lookup its genome position by rs number.

	Take rs1006094 as an example:		Take rs1006094 as an example:
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	== Resources ==		== Resources ==
	* liftRsNumber.py [~~[Media: liftRsNumber.py]~~]		* liftRsNumber.py []
	* liftMap.py [~~[Media: liftMap.py~~]		* liftMap.py []
	* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]		* NCBI provisional map [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.txt.gz file] and [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/misc/exchange/Remap_36_3_37_1.info info]
	* NCBI RgMergeArch file and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]		* NCBI RgMergeArch [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/RsMergeArch.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=RsMergeArch schema]
	* NCBI SNPHistory file and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]		* NCBI SNPHistory [ftp://ftp.ncbi.nih.gov:/snp/organisms/human_9606/database/organism_data/SNPHistory.bcp.gz file] and [http://www.ncbi.nlm.nih.gov/SNP/snp_db_table_description.cgi?t=SNPHistory schema]
	* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]		* How UCSC dbSNP differs from NCBI dbSNP [http://genomewiki.ucsc.edu/index.php/DbSNP_Track_Notes UCSC dbSNP track note]
	* The dbSNP mapping process [http://www.ncbi.nlm.nih.gov/books/NBK44455/ link]		* The dbSNP mapping process [http://www.ncbi.nlm.nih.gov/books/NBK44455/ link]