Intern - Revision history

Albrecht: /* liftover a plink file */

2014-09-24T13:02:34Z

liftover a plink file

← Older revision		Revision as of 15:02, 24 September 2014
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	echo The new plink file is called ${Files}Hg19 and are on the same strand as the original file		echo The new plink file is called ${Files}Hg19 and are on the same strand as the original file
	#flip strands		#flip strands
	cat ${Files}Hg19.bedfile \| grep \-$ \| cut -f4 > flipSNPs.txt		cat ${Files}Hg19.bedfile \| grep -w \- \| cut -f4 > flipSNPs.txt
	$plink --noweb --ped ${Files}Red.ped --map hg19.map --flip flipSNPs.txt --recode --make-bed --out ${Files}Hg19		$plink --noweb --ped ${Files}Red.ped --map hg19.map --flip flipSNPs.txt --recode --make-bed --out ${Files}Hg19
	#$plink --noweb --bfile ${Files}Hg19 --recode --out ${Files}Hg19		#$plink --noweb --bfile ${Files}Hg19 --recode --out ${Files}Hg19

Albrecht: /* liftover a plink file */

2014-09-24T12:55:48Z

liftover a plink file

← Older revision		Revision as of 14:55, 24 September 2014
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	echo The new plink file is called ${Files}Hg19 and are on the same strand as the original file		echo The new plink file is called ${Files}Hg19 and are on the same strand as the original file
	#flip strands		#flip strands
	cat ${Files}Hg19.bedfile \| grep \- \| cut -f4 > flipSNPs.txt		cat ${Files}Hg19.bedfile \| grep \-$ \| cut -f4 > flipSNPs.txt
	$plink --noweb --ped ${Files}Red.ped --map hg19.map --flip flipSNPs.txt --recode --make-bed --out ${Files}Hg19		$plink --noweb --ped ${Files}Red.ped --map hg19.map --flip flipSNPs.txt --recode --make-bed --out ${Files}Hg19
	#$plink --noweb --bfile ${Files}Hg19 --recode --out ${Files}Hg19		#$plink --noweb --bfile ${Files}Hg19 --recode --out ${Files}Hg19

Albrecht: /* liftover a plink file */

2014-09-18T09:21:09Z

liftover a plink file

← Older revision		Revision as of 11:21, 18 September 2014
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	Note that if two SNP map to the same position after liftover one of them is removed.		Note that if two SNP map to the same position after liftover one of them is removed.
	<pre>		<pre>

	#!/bin/bash		#!/bin/bash
	#make liftover file		#make liftover file
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	echo "supply a plink prefix"		echo "supply a plink prefix"
	exit		exit
	fi

	~~if [ -f $Files.map ]~~
	~~then~~
	~~echo using file $Files.map~~
	~~else~~
	~~echo the file ${Files}.map does not exists $use plink --recode$~~
	fi		fi

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	echo the file $Files.bed does not exists $use plink --make-bed$		echo the file $Files.bed does not exists $use plink --make-bed$
	fi		fi

	#make bed file for liftover		#make bed file for liftover
	Rscript -e "options(scipen=10);map<-read.table('$Files.~~map~~',hea=F,as.is=T);res<-cbind(paste('chr',map[,1],sep=''),map[,4]-1,map[,4],map[,2],0,'+');write.table(res,file='$Files.bedfile',col=F,row=F,qu=F,sep='\t')"		Rscript -e "options(scipen=10);map<-read.table('$Files.bim',hea=F,as.is=T);res<-cbind(paste('chr',map[,1],sep=''),map[,4]-1,map[,4],map[,2],0,'+');write.table(res,file='$Files.bedfile',col=F,row=F,qu=F,sep='\t')"

	#liftover		#liftover
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	cat ${Files}Hg19.bedfile \| grep \- \| cut -f4 > flipSNPs.txt		cat ${Files}Hg19.bedfile \| grep \- \| cut -f4 > flipSNPs.txt
	$plink --noweb --ped ${Files}Red.ped --map hg19.map --flip flipSNPs.txt --recode --make-bed --out ${Files}Hg19		$plink --noweb --ped ${Files}Red.ped --map hg19.map --flip flipSNPs.txt --recode --make-bed --out ${Files}Hg19
	$plink --noweb --bfile ${Files}Hg19 --recode --out ${Files}Hg19		#$plink --noweb --bfile ${Files}Hg19 --recode --out ${Files}Hg19
	</pre>		</pre>

Line 250:		Line 245:

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


	==plot admix results==		==plot admix results==

Albrecht: /* ieatgor */

2014-07-03T15:19:28Z

ieatgor

← Older revision		Revision as of 17:19, 3 July 2014
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	==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 /home/software/public/software/intern/ieatgor/ieatgor on pontus
			to compile see header of most recent version (V3)


	~~to compile~~
	<pre>		<pre>
	~~g++~~ -O3 -~~o ieatgor ieatgor.cpp~~ -lz		./ieatgor

			RUN: ieatgor <targetFile> <file> OPTIONS

			target file format: chrName:start-end

			OPTIONS:
			-offset INT offset the target positions by INT
			-skip INT number of lines to skip (will be printet)
			-num INT are the chromosome in lexical (default 0) or numeric (1) order

	</pre>		</pre>

	The target file must be sorted. example of target file
			The target file must be sorted in the same order as the file you want to extract from (gor file). example of target file
	<pre>		<pre>
	chr1:22323:232322		chr1:22323:232322
Line 107:		Line 119:
	</pre>		</pre>

	A "gor" file is a file with the first ~~coloum~~ being the chromosome and the second ~~coloum~~ being the positions. The rest of the ~~coloums~~ are not important. The gor file must be sorted based on the positions and chr. gz gor files are also accepted.
			A "gor" file is a file with the first column being the chromosome and the second column being the positions. The rest of the columns are not important. The gor file must be sorted based on the positions and chr. gz gor files are also accepted. The sorting must be lexical or numeric
	example of a gor file		example of a gor file
	<pre>		<pre>
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	./ieatgor file.target file.gor		./ieatgor file.target file.gor
	</pre>		</pre>
	the extracted line are returned to standard out.		the extracted line are returned to standard out.

	==getliner==		==getliner==

Albrecht at 14:01, 20 March 2014

2014-03-20T14:01:13Z

← Older revision		Revision as of 16:01, 20 March 2014
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	This sofware is for internal use. If you found this page then 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.		This sofware is for internal use. If you found this page then congrats. Feel free you use the methods but they might not work, give wrong results or other nasty stuff. If and when they fuck up don't contact us or complain.

	=Secret software=		=Secret software=

Albrecht at 14:00, 20 March 2014

2014-03-20T14:00:55Z

← Older revision		Revision as of 16:00, 20 March 2014
Line 1:		Line 1:
	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.		This sofware is for internal use. If you found this page then 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: /* plot LD region from plink file */

2014-03-20T14:00:41Z

plot LD region from plink file

← Older revision		Revision as of 16:00, 20 March 2014
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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)

	~~<pre>~~
	~~library(snpMatrix,lib="/home/albrecht/R/x86_64-pc-linux-gnu-library/2.15/")~~
	~~</pre>~~

	===R function===		===R function===

Thorfinn: /* Technics */

2014-03-20T13:59:40Z

Technics

← Older revision		Revision as of 15:59, 20 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==

Thorfinn: /* Secret software */

2014-03-20T13:37:00Z

Secret software

← Older revision		Revision as of 15:37, 20 March 2014
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	Extract bases from a fasta file		Extract bases from a fasta file

			==[[Getinsertsize]]==

			Get an estimate of the insert sizes, and read lengths.

	=Other stuff=		=Other stuff=

Thorfinn: /* Download */

2014-03-20T10:00:11Z

Download

← Older revision		Revision as of 12:00, 20 March 2014
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	===Download===		===Download===

	[[bambi.tar.gz]]		[[http://www.popgen.dk/software/download/bambi.tar.gz]]

	===Usage===		===Usage===
	Program is invoked with either:		Program is invoked with either: