Abbababa - Revision history

Albrecht at 09:46, 11 March 2016

2016-03-11T09:46:18Z

@@ Line 57: / Line 57: @@
 ;*.abbbababa
 Output: Each lines represents a block with a chromsome name (Column 1), a start position (Column 2), an end postion (Column 3). The new columns are the counts of ABBA and BABA sites. For each combination of 3 individuals (H1,H2,H3) two columns are printed. These number served as input to the R script called jackKnife.R. This script will skip combinations of individuals if there is less than 3 blocks with data. Type "Rscript R/jackKnife.R" to see additional options.
 ==Example==
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 '''Z''' Z value that can be used to determine the significance of the test. As in Reich et al. an absolute value of the Z score above 3 is often used as a critical value. However, this note that this does not take into account the fact that we perform multiple tests.

2016-02-15T09:21:19Z

← Older revision		Revision as of 11:21, 15 February 2016
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	Performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology). As all methods in ANGSD we require that the header of the BAM files are the same.		Performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology). As all methods in ANGSD we require that the header of the BAM files are the same.

	;~~BUG!~~ if you use -rf to specify regions. These MUST appear in the same ordering as your fai file.		; some of the options only works for the develupmental version availeble from github
			; if you use -rf to specify regions. These MUST appear in the same ordering as your fai file.

	__TOC__		__TOC__

2016-01-22T12:35:42Z

Options

← Older revision		Revision as of 14:35, 22 January 2016
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	use -doCounts 1 in order to count the bases at each sites after filters.		use -doCounts 1 in order to count the bases at each sites after filters.
	; -useLast [int]		; -useLast [int]
	use the last individual in the bam file list as outgroup instead of a fasta file (-anc)		1: use the last individual in the bam file list as outgroup instead of a fasta file (-anc)
	; -enhance [int]		; -enhance [int]
	1: use only sites where the reads for the outgroup has the same base for all reads. Only works with -useLast 1		1: use only sites where the reads for the outgroup has the same base for all reads. Only works with -useLast 1

2016-01-22T12:35:17Z

← Older revision		Revision as of 14:35, 22 January 2016
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	--------------		--------------
	~~analysisAbbababa~~.cpp:		abcDstat.cpp:
	-doAbbababa 0 run the abbababa analysis		-doAbbababa 0 run the abbababa analysis
	-rmTrans 0 remove transitions		-rmTrans 0 remove transitions
	-blockSize 5000000 size of each block in bases		-blockSize 5000000 size of each block in bases
	-~~anc~~ (null) fasta file with outgroup		-enhance 0 outgroup must have same base for all reads
			-ans (null) fasta file with outgroup
			-useLast 0 use the last individuals as outgroup instead of -anc
	</pre>		</pre>

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	; -doCounts 1		; -doCounts 1
	use -doCounts 1 in order to count the bases at each sites after filters.		use -doCounts 1 in order to count the bases at each sites after filters.
			; -useLast [int]
			use the last individual in the bam file list as outgroup instead of a fasta file (-anc)
			; -enhance [int]
			1: use only sites where the reads for the outgroup has the same base for all reads. Only works with -useLast 1

2016-01-22T10:01:06Z

Example

← Older revision		Revision as of 12:01, 22 January 2016
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	<pre>		<pre>
			# select 5 individuals
	head -n5 bam.filelist > smallBam.filelist		head -n5 bam.filelist > smallBam.filelist

			#run angsd
	./angsd -out out -doAbbababa 1 -bam smallBam.filelist -doCounts 1 -anc chimpHG19.fa		./angsd -out out -doAbbababa 1 -bam smallBam.filelist -doCounts 1 -anc chimpHG19.fa

			#estimate Z score
	Rscript R/jackKnife.R file=out.abbababa indNames=smallBam.filelist outfile=out		Rscript R/jackKnife.R file=out.abbababa indNames=smallBam.filelist outfile=out
	</pre>		</pre>

2015-11-16T13:04:16Z

← Older revision		Revision as of 15:04, 16 November 2015
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	Performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology). As all methods in ANGSD we require that the header of the BAM files are the same.		Performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology). As all methods in ANGSD we require that the header of the BAM files are the same.

			;BUG! if you use -rf to specify regions. These MUST appear in the same ordering as your fai file.

	__TOC__		__TOC__

2014-02-26T11:19:58Z

Options

← Older revision		Revision as of 13:19, 26 February 2014
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	;-doAbbababa 1: sample a random base at each position.		;-doAbbababa 1: sample a random base at each position.

	;-rmTrans		;-rmTrans [int]
	Remove transitions (important for ancient DNA)		0; use all reads (default), 1 Remove transitions (important for ancient DNA)
	;-blockSize [INT]		;-blockSize [INT]
	Size of each block. Choose a number that is higher than the LD in the populations. For human 5Mb (5000000) is usually used.		Size of each block. Choose a number that is higher than the LD in the populations. For human 5Mb (5000000) is usually used.

2014-02-07T13:16:45Z

Output

← Older revision		Revision as of 15:16, 7 February 2014
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	=Output=		=Output=
	;*.abbbababa		;*.abbbababa
	Output: Each lines represents a block with a chromsome name (Column 1), a start position (Column 2), an end postion (Column 3). The new columns are the counts of ABBA and BABA sites. For each combination of 3 individuals (H1,H2,H3) two columns are printed. These number served as input to the R script called jackKnife.R. This script will skip combinations of individuals if there is less than 3 blocks with data.		Output: Each lines represents a block with a chromsome name (Column 1), a start position (Column 2), an end postion (Column 3). The new columns are the counts of ABBA and BABA sites. For each combination of 3 individuals (H1,H2,H3) two columns are printed. These number served as input to the R script called jackKnife.R. This script will skip combinations of individuals if there is less than 3 blocks with data. Type "Rscript R/jackKnife.R" to see additional options.

	==Example==		==Example==

2014-02-07T13:15:10Z

Output

← Older revision		Revision as of 15:15, 7 February 2014
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	=Output=		=Output=
	;*.abbbababa		;*.abbbababa
	Output: Each lines represents a block with a chromsome name (Column 1), a start position (Column 2), an end postion (Column 3). The new columns are the counts of ABBA and BABA sites. For each combination of 3 individuals (H1,H2,H3) two columns are printed. These number served as input to the R script called jackKnife.R		Output: Each lines represents a block with a chromsome name (Column 1), a start position (Column 2), an end postion (Column 3). The new columns are the counts of ABBA and BABA sites. For each combination of 3 individuals (H1,H2,H3) two columns are printed. These number served as input to the R script called jackKnife.R. This script will skip combinations of individuals if there is less than 3 blocks with data.

	==Example==		==Example==
	Create a fasta file bases from a random samples of bases.		Create a fasta file bases from a random samples of bases.

2014-01-08T13:20:55Z

Brief Overview

← Older revision		Revision as of 15:20, 8 January 2014
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	-rmTrans 0 remove transitions		-rmTrans 0 remove transitions
	-blockSize 5000000 size of each block in bases		-blockSize 5000000 size of each block in bases
	-~~ans~~ (null) fasta file with outgroup		-anc (null) fasta file with outgroup

	</pre>		</pre>