RefFinder - Revision history

Thorfinn: Reverted edits by Albrecht (talk) to last revision by Thorfinn

2014-03-20T13:55:06Z

Reverted edits by Albrecht (talk) to last revision by Thorfinn

Albrecht: /* Stand alone */

2014-03-19T15:05:14Z

Stand alone

← Older revision		Revision as of 17:05, 19 March 2014
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	cd ..		cd ..
	</pre>		</pre>

	~~=Stand alone=~~
	This sofware is for internal use. If you found this page den congrats. Feel free you use the methods but they might not work, give wrong results or other nasty stuff. If and then they fuck up don't contact us or complain.

	=Secret software=		=Secret software=

Albrecht at 15:04, 19 March 2014

2014-03-19T15:04:40Z

← Older revision		Revision as of 17:04, 19 March 2014
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	</pre>		</pre>

	** Technics		==Technics==
	Program spawns a single thread, when a chunk has been read, and the thread is not finished it will wait.		Program spawns a single thread, when a chunk has been read, and the thread is not finished it will wait.


	* ieatgor		==ieatgor==

	Extract lines from file in "gor" format. The files can be found in this [[ieatgor/][folder]]		Extract lines from file in "gor" format. The files can be found in this [[ieatgor/][folder]]
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	the extracted line are returned to standard out.		the extracted line are returned to standard out.

	* getliner		==getliner==
	NB HUGE BUG, must +1 when using -l and zipped files. Sorry for inconveincace. (tsk)		NB HUGE BUG, must +1 when using -l and zipped files. Sorry for inconveincace. (tsk)

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	* calcABBABABA		==calcABBABABA==

	This is program that calculates ABBA-BABA related stats for a given chromosome.		This is program that calculates ABBA-BABA related stats for a given chromosome.
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	The program outputs three files: an abbababa file (with only abbababa stats), a count file (with overall counts for the chromosome) and a summary file where the compile time, run time and the cmds and the input files used when the program was run are all listed.		The program outputs three files: an abbababa file (with only abbababa stats), a count file (with overall counts for the chromosome) and a summary file where the compile time, run time and the cmds and the input files used when the program was run are all listed.

	* plot Plink		==plot Plink==

	[[Rfun/][Folder]]		[[Rfun/][Folder]]
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	</pre>		</pre>

			==liftover a plink file==
	* ngsAdmix

	*** download

	~~[[ngsAdmix/][Download folder]]~~

	~~Download path~~
	~~<pre>~~
	~~/home/software/public/software/intern/ngsAdmix/~~
	~~</pre>~~

	*** compile
	~~compile with icpc or g++ (icpc much better)~~
	~~<pre>~~
	~~icpc -O3 -o ngsAdmix ngsAdmix12.cpp -lz -pthread~~
	~~g++ -O3 -o ngsAdmix ngsAdmix12.cpp -lz -pthread~~
	~~</pre>~~

	*** options
	~~options are shown with~~
	~~<pre>~~
	~~./ngsAdmix~~
	~~</pre>~~
	~~All options also have a short form (first letter)~~

	~~- default stopping criteria is either tolerence 0.0001 for emSq~~
	~~- default stopping criteria is difference in loglikelihoods of 0.1 over 50 iterations for both em and emSq~~
	~~- default optimaziation is emSq~~

	*** run example
	~~<pre>~~
	~~./ngsAdmix -l dat.beagle -i 5000 -K 3 -P 5 -m 1 -o datK3~~
	~~</pre>~~


	* liftover a plink file


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	</pre>		</pre>

	~~***~~ run ~~pre~~		===run exampe===
	<pre>		<pre>
	./liftover.sh myPlinkFile		./liftover.sh myPlinkFile
	</pre>		</pre>

	* angsd		==angsd==

	[[angsd/][Download folder]]		[[angsd/][Download folder]]


	* plot admix results		==plot admix results==

	~~***~~ Download		===Download===

	[[Rfun/plotAdmix_anders.R][Get the R script]]		[[Rfun/plotAdmix_anders.R][Get the R script]]
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	* plot LD region from plink file		==plot LD region from plink file==

	plot the LD in a region. You need SNPmatrix working. If you cannot get SNPmatrix to work use Relate instead (ldsnp3 function) or if on pontus use		plot the LD in a region. You need SNPmatrix working. If you cannot get SNPmatrix to work use Relate instead (ldsnp3 function) or if on pontus use
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	<include file="andersLink/ldplot.R" markup="example">		<include file="andersLink/ldplot.R" markup="example">

	~~***~~ example		===example===
	<pre>		<pre>
	library(snpMatrix)		library(snpMatrix)

Albrecht: /* Example */

2014-03-19T15:01:44Z

Example

Show changes

Thorfinn: /* API */

2014-03-13T13:26:43Z

API

← Older revision		Revision as of 15:26, 13 March 2014
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	g++ sampleProg.cpp refFinder.o -lz		g++ sampleProg.cpp refFinder.o -lz
	</pre>		</pre>

			=bugs=
			# do check if reference file doesn't exist.

Thorfinn: /* Install */

2014-03-13T13:20:55Z

Install

← Older revision		Revision as of 15:20, 13 March 2014
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	<pre>		<pre>
	wget http://popgen.dk/software/download/refFinder/refFinder.tar.gz		wget http://popgen.dk/software/download/refFinder/refFinder.tar.gz
			tar xf refFinder.tar.gz
	cd refFinder/		cd refFinder/
	make		make

Thorfinn: /* API */

2014-03-13T13:14:44Z

API

← Older revision		Revision as of 15:14, 13 March 2014
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	</pre>		</pre>

	Remember to link with refFinder~~.o faidx.o razf~~.o and -lz		Remember to link with refFinder.o and -lz

	<pre>		<pre>
	g++ sampleProg.cpp refFinder~~.o faidx.o razf~~.o -lz		g++ sampleProg.cpp refFinder.o -lz
	</pre>		</pre>

Thorfinn: /* Example */

2014-03-13T13:14:09Z

Example

← Older revision		Revision as of 15:14, 13 March 2014
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	<pre>		<pre>
	cut -f1-2 ../angsd/test/small.sam \|./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst		cut -f1-2 ../angsd/test/small.sam \|./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst
	cmp tst ../angsd/test/small.~~bam~~		cmp tst ../angsd/test/small.sam
	</pre>		</pre>

Thorfinn: /* Example */

2014-03-13T13:13:26Z

Example

← Older revision		Revision as of 15:13, 13 March 2014
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	<pre>		<pre>
	cut -f1-2 ../angsd/test/small.sam \|./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst		cut -f1-2 ../angsd/test/small.sam \|./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst
	cmp tst small.bam		cmp tst ../angsd/test/small.bam
	</pre>		</pre>

Thorfinn: /* API */

2014-03-13T11:48:36Z

API

← Older revision		Revision as of 13:48, 13 March 2014
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	perFasta *pf = init("hg19.fa");		perFasta *pf = init("hg19.fa");
	char refbase = getchar("chr20",130224101,pf)		char refbase = getchar("chr20",130224101,pf)
			//refbase now contains the reference base for chr20 at position 130,224,101
	destroy(pf);		destroy(pf);
	</pre>		</pre>