Abbababa2

The ABBABABA (multipop) compute the abbababa test (aka D-statistic), that means testing for an ancient admixture (or wrong tree topology). Differently from ABBABABA (D_stat) multiple individuals for each one of the groups are allowed. As all methods in ANGSD we require that the header of the BAM files are the same.

some of the options only works for the developmental version availeble from github

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

<classdiagram type="dir:LR">

[*.bam and/or *.cram| NGS genome datasets{bg:orange}]->[Sequence data|All bases or Random bases]

[Sequence data]->[Elaborate multiple genomes per population] [Sequence data]->[*.abbababa2counts|ABBA and BABA intermediate counts file {bg:blue}] [Elaborate multiple genomes per population]->[*.abbababa2|weighted ABBA and BABA counts file {bg:blue}] </classdiagram>

<classdiagram type="dir:LR"> [*.abbababa2|weighted ABBA and BABA counts file {bg:blue}]->estAvgError.R[*.Observed.txt|Observed D stat and Z scores{bg:blue}] [*.abbababa2|weighted ABBA and BABA counts file {bg:blue}]->estAvgError.R[*.ErrorCorr.txt|D stat and Z scores Error Corrected{bg:blue}] [*.abbababa2|weighted ABBA and BABA counts file {bg:blue}]->estAvgError.R[*.TransRemErrorCorr.txt|D stat and Z scores Error Corrected with ancient Transition Removal{bg:blue}] [*.abbababa2|weighted ABBA and BABA counts file {bg:blue}]->estAvgError.R[*.TransRem.txt|D stat and Z scores with Transition Removal{bg:blue}] </classdiagram>

Method

Brief Overview

> ./angsd -doAbbababa2

--------------
abcDstat2.cpp:
	-doAbbababa2	                0	run the abbababa analysis
	-rmTrans		        0       remove transitions
	-blockSize		       5000000	size of each block in bases
	-anc			       (null)	fasta file with outgroup
	-sample			        0	sample a single base in each individual
	-maxDepth		        100	max depth of each site allowed
	-sizeH1			        1	num of individuals in group H1
	-sizeH2			        1	num of individuals in group H2
	-sizeH3			        1	num of individuals in group H3
	-sizeH4			        1	num of individuals in group H4
	-enhance			0	only analyze sites where outgroup H4 is non poly
	-Aanc			        0	set H4 outgroup allele as A in each site
	-combFile		        0	create an optional *.abbababa2counts file where are printed the 
                                     numbers of alleles combinations without having weighted the individuals

This function will counts the number of ABBA and BABA sites.

Options

-doAbbababa2 1

take all bases at each position.

-rmTrans [int]

0; use all reads (default), 1 Remove transitions (important for ancient DNA)

-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.

-anc [fileName.fa]

Include an outgroup in fasta format.

-doCounts 1

use -doCounts 1 in order to count the bases at each sites after filters.

-enhance [int]

1: use only sites where the reads for the outgroup has the same base for all reads (If you want to use it, it must be only when you have one genome in the outgroup, it won't work otherwise).

-sample [int]

1: sample only one base at each position for every individual 0: all bases at each position are used for the ABBABABA test

-maxDepth [int]

allows for a maximum depth in each site to avoid overflow of the ABBA BABA counts

-sizeH* [int]

decide how many individuals are in each group (the file list must contain the BAM files ordered from population 1 to 4). If you are using a fasta file (option -anc) for population H4, leave -sizeH4 at its default value

-Aanc [int]

1: H4 allele is A in each site.

-combFile [int]

1: create an intermediate *.abbababa2counts to obtain the allele events before weighting the samples (however, this file is not used for the estimation of the D-statistic).

In order to do fancy filtering of bases based on quality scores see the Allele counts options.

Output

• .abbbababa2

Output: Each line 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 all 256 counted combination of alleles, starting from X0000=AAAA,X0001=AAAC,....,X3333=TTTT, with the correspondence 0=A,1=C,2=G,3=T. This file is used as input for the R script estAvgError.R. Type "Rscript R/estAvgError.R" to see additional options.

• .abbbababa2counts (optional file)

Output: As above each line 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 all 256 counted combination of alleles, starting from X0000=AAAA,X0001=AAAC,....,X3333=TTTT, with the correspondence 0=A,1=C,2=G,3=T. This file is not used as input for the ABBABABA test.

Example

Run the ABBABABA (multipop), without sampling a single allele for each site. We use 2 individuals for each group, thus the smallBam.filelist file contains the 8 file names ordered from population H1 to H4.

# select 8 individuals (suppose they are already in the desired order H1,..,H4)
head -n8 bam.filelist > smallBam.filelist

#run angsd
./angsd -out out -doAbbababa2 1 -bam smallBam.filelist -doCounts 1 -sample 0 -enhance 0 -sizeH1 2 -sizeH2 2 -sizeH3 3 -sizeH4 2 -combFile 0

#estimate Z score
Rscript R/estAvgError.R file=out outfile=outDstat

This results in multiple output files with all the results.

1) a file outDstatStd.txt, that contains the results of the ABBABABA test without applying neither error correction or ancient transition removal

2) a file outDstatNoErrorNoTrans.txt, that contains the results of the ABBABABA test without applying error correction but removing ancient transitions

Output

1)outDstatStd.txt

mean(D)          JK-D          V(JK-D)            Z            pvalue           nABBA         nBABA          nBBAA
-0.042874       -0.042945       0.000643        -1.690314       0.090968        1697.447933     1704.675933     6374.948767	

2)outDstatNoErrorNoTrans.txt

mean(D)          JK-D          V(JK-D)            Z            pvalue           nABBA         nBABA          nBBAA
-0.042874       -0.042945       0.000643        -1.690314       0.090968        1697.447933     1704.675933     6374.948767	

mean(D) The average of test statistics: (nABBA-nBABA)/(nABBA+nBABA), each one calculated for a block of data.

JK-D The estimated test statistic: (nABBA-nBABA)/(nABBA+nBABA) after being bias corrected. This value should be similar to the one in column 1. A negative value means that H1 is closer to H3 than H2 is. A positive value means that H2 is closer to H3 than H1 is.

V(JK-D) estimated m-delete blocked Jackknife variance of the estimator of column 2. It's used to compute the Z-value.

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.

pvalue p-value corresponding to Z for a double-sided standard test. the critical value 0.001 correspond to the value of Z=3.

nABBA the total counts of ABBA patterns

nBABA the total counts of BABA patterns

nBBAA the total counts of BBAA patterns