Revision as of 18:13, 2 December 2013

Available from version 0.559+.

performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology)

[BAM files{bg:orange}]->[Sequence data|Random base]

[sequence data]->[*.abbababa|ABBA and BABA couts file{bg:blue}] </classdiagram>

<classdiagram type="dir:LR"> [*.abbababa|ABBA and BABA couts file{bg:blue}]->jackKnife.R[D stat and Z scores{bg:blue}] </classdiagram>

Brief Overview

> ./angsd -doAbbababa

--------------
analysisAbbababa.cpp:
	-doAbbababa	0
	1: use a random base
	-rmTrans		0	remove transitions
	-blockSize		5000000	number of based in a block

This function will counts the number of ABBA and BABA sites

Options

-doAbbababa 1: sample a random base at each position.

-rmTrans

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.

Output

.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

Example

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

head -n5 smallBam.filelist > smallerBam.filelist
./angsd -out out -doAbbababa 1 -bam smallerBam.filelist -doCounts 1 -anc /space/genomes/refgenomes/ancestral/hg19/fasta/hg19ancNoChr.fa
Rscript file=out.abbababa indNames=smallerBam.filelist

@@ Line 4: / Line 4: @@
 <classdiagram type="dir:LR">
-  [Single BAM file{bg:orange}]->[Sequence data|Random base (-doAbbababa 1)]
+  [BAM files{bg:orange}]->[Sequence data|Random base]
 [sequence data]->[*.abbababa|ABBA and BABA couts file{bg:blue}]
 </classdiagram>
@@ Line 29: / Line 29: @@
 =Options=
-;-doFasta 1: sample a random base at each position.
+;-doAbbababa 1: sample a random base at each position.
-;-minQ [INT]
+;-rmTrans
-minimum base quality score.
+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.
 =Output=
-Output is a fasta file, a normal looking fast file. Nothing special about this. For -doFasta 1, sometimes its big letters sometime small letters. This is due to the results being copied directly from the sequencing data. So small/big letters correspond to which strand for the original data. For the consensus fasta all letters are capital letters.
+;*.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
 ==Example==
 Create a fasta file bases from a random samples of bases.
 <pre>
-./angsd -i smallNA07056.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -doFasta 1
+head -n5 smallBam.filelist > smallerBam.filelist
+./angsd -out out -doAbbababa 1 -bam smallerBam.filelist -doCounts 1 -anc /space/genomes/refgenomes/ancestral/hg19/fasta/hg19ancNoChr.fa
+Rscript file=out.abbababa indNames=smallerBam.filelist
 </pre>

Abbababa: Difference between revisions

Revision as of 18:13, 2 December 2013

Contents

Brief Overview

Options

Output

Example

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