Quick Start - Revision history

Thorfinn at 12:58, 4 December 2015

2015-12-04T12:58:36Z

← Older revision		Revision as of 14:58, 4 December 2015
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	This page all contain some random examples that shows some aspect of the ANGSD program. We assume you will have SAMtools installed for general BAM/~~CRAMmanipulation~~		This page all contain some random examples that shows some aspect of the ANGSD program. We assume you will have SAMtools installed for general BAM/CRAM manipulation

	Many of the examples in the individual subpages are based on this test data set. The examples below are just some random examples.		Many of the examples in the individual subpages are based on this test data set. The examples below are just some random examples.

Thorfinn at 12:58, 4 December 2015

2015-12-04T12:58:29Z

← Older revision		Revision as of 14:58, 4 December 2015
Line 1:		Line 1:
	This page all contain some random examples that shows some aspect of the ANGSD program. We assume you will have SAMtools installed for general ~~bam~~/~~cram manipulation~~		This page all contain some random examples that shows some aspect of the ANGSD program. We assume you will have SAMtools installed for general BAM/CRAMmanipulation

	Many of the examples in the individual subpages are based on this test data set. The examples below are just some random examples.		Many of the examples in the individual subpages are based on this test data set. The examples below are just some random examples.

Albrecht at 09:20, 4 December 2015

2015-12-04T09:20:47Z

← Older revision		Revision as of 11:20, 4 December 2015
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	Notice that the 'marker' contains the genomic position, encoded by using underscore as separator.		Notice that the 'marker' contains the genomic position, encoded by using underscore as separator.

	~~=Finding the SFS=~~
	~~There is a full example of estimating the site frequency spectrum [[SFS_Estimation#Example]]. We even have an example of estimating the folded spectrum [[SFS_Estimation#Folded_spectra]]~~
	~~=Estimating thetas, neutrality test statistics=~~
	~~We also have working example for performing theta estimation.~~
	~~http://www.popgen.dk/angsd/index.php/Tajima#Example~~

Albrecht: /* Examples */

2015-12-04T09:19:51Z

Examples

← Older revision		Revision as of 11:19, 4 December 2015
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	==Generate Beagle Likelihood files==		==Generate Beagle Likelihood files==
	For diploid samples we have 10 possible genotypes. but we would only expect to observe two different alleles at most sites. We can infer the major and minor allele and output the 3 possible genotypes in beagle genotype likelihood format. Furthermore we are only interested in variable sites, so let us use the LRT statistic for filtering out the sites that are very likely to be polymorphic with a p-value less than 10^-6. We need to allele frequency in order to test if a site is polymorphic~~. The default behaviour for -doMaf is to output a file, but we are not interested in frequency estimates so we can disable the MAF output by making it negative~~.		For diploid samples we have 10 possible genotypes. but we would only expect to observe two different alleles at most sites. We can infer the major and minor allele and output the 3 possible genotypes in beagle genotype likelihood format. Furthermore we are only interested in variable sites, so let us use the LRT statistic for filtering out the sites that are very likely to be polymorphic with a p-value less than 10^-6. We need to allele frequency in order to test if a site is polymorphic.

	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	./angsd -GL 2 -doGlf 2 -b bam.filelist -doMajorMinor 1 -SNP_pval 1e-6 -doMaf -1		./angsd -GL 2 -doGlf 2 -b bam.filelist -doMajorMinor 1 -SNP_pval 1e-6 -doMaf 1
	<pre class="mw-collapsible-content">		<pre class="mw-collapsible-content">
	Command:		Command:
	./angsd -GL 2 -doGlf 2 -b bam.filelist -doMajorMinor 1 -SNP_pval 1e-6 -doMaf -1		./angsd -GL 2 -doGlf 2 -b bam.filelist -doMajorMinor 1 -SNP_pval 1e-6 -doMaf 1
	-> angsd version: 0.574 build(Jan 10 2014 17:44:41)		-> angsd version: 0.574 build(Jan 10 2014 17:44:41)
	-> No '-out' argument given, output files will be called 'angsdput'		-> No '-out' argument given, output files will be called 'angsdput'
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	Notice that the 'marker' contains the genomic position, encoded by using underscore as separator.		Notice that the 'marker' contains the genomic position, encoded by using underscore as separator.


	=Finding the SFS=		=Finding the SFS=

Albrecht: /* Ancestral fasta file for hg19 */

2015-12-04T08:56:48Z

Ancestral fasta file for hg19

← Older revision		Revision as of 10:56, 4 December 2015
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	If you want to run the SFS examples on the wiki you should also download the ancestral states for the hg19 assembly of the human genome.		If you want to run the SFS examples on the wiki you should also download the ancestral states for the hg19 assembly of the human genome.
	<pre>		<pre>
	wget http://popgen.dk/software/download/angsd/hg19ancNoChr.fa		wget http://popgen.dk/software/download/angsd/hg19ancNoChr.fa.gz
	mv hg19ancNoChr.fa chimpHg19.fa		mv hg19ancNoChr.fa.gz chimpHg19.fa.gz
	samtools faidx chimpHg19.fa		samtools faidx chimpHg19.fa.gz
	</pre>		</pre>
	NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the compressed .fa file here:		NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the compressed .fa file here:

Albrecht at 08:52, 4 December 2015

2015-12-04T08:52:56Z

← Older revision		Revision as of 10:52, 4 December 2015
Line 1:		Line 1:
	This page all contain some random examples that shows some aspect of the ANGSD program. We assume you will have SAMtools installed.		This page all contain some random examples that shows some aspect of the ANGSD program. We assume you will have SAMtools installed for general bam/cram manipulation

	Many of the examples in the individual subpages are based on this test data set. The examples below are just some random examples.		Many of the examples in the individual subpages are based on this test data set. The examples below are just some random examples.

Thorfinn: /* Ancestral fasta file for hg19 */

2014-07-22T19:04:56Z

Ancestral fasta file for hg19

← Older revision		Revision as of 21:04, 22 July 2014
Line 29:		Line 29:
	samtools faidx chimpHg19.fa		samtools faidx chimpHg19.fa
	</pre>		</pre>
	NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the ~~big~~ .fa file here:		NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the compressed .fa file here:
	http://dna.ku.dk/~thorfinn/hg19ancNoChr.fa.gz		http://dna.ku.dk/~thorfinn/hg19ancNoChr.fa.gz

Thorfinn: /* Ancestral fasta file for hg19 */

2014-07-22T19:02:55Z

Ancestral fasta file for hg19

← Older revision		Revision as of 21:02, 22 July 2014
Line 30:		Line 30:
	</pre>		</pre>
	NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the big .fa file here:		NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the big .fa file here:
	http://dna.ku.dk/~thorfinn/hg19ancNoChr.fa		http://dna.ku.dk/~thorfinn/hg19ancNoChr.fa.gz

	=Examples=		=Examples=

Thorfinn: /* Ancestral fasta file for hg19 */

2014-07-22T18:49:12Z

Ancestral fasta file for hg19

← Older revision		Revision as of 20:49, 22 July 2014
Line 29:		Line 29:
	samtools faidx chimpHg19.fa		samtools faidx chimpHg19.fa
	</pre>		</pre>
			NB some have complained that the popgen.dk server is unstable, and we are therefore also hosting the big .fa file here:
			http://dna.ku.dk/~thorfinn/hg19ancNoChr.fa

	=Examples=		=Examples=

Thorfinn: /* Estimating thetas, neutrality test statistics */

2014-06-30T12:14:41Z

Estimating thetas, neutrality test statistics

← Older revision		Revision as of 14:14, 30 June 2014
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	There is a full example of estimating the site frequency spectrum [[SFS_Estimation#Example]]. We even have an example of estimating the folded spectrum [[SFS_Estimation#Folded_spectra]]		There is a full example of estimating the site frequency spectrum [[SFS_Estimation#Example]]. We even have an example of estimating the folded spectrum [[SFS_Estimation#Folded_spectra]]
	=Estimating thetas, neutrality test statistics=		=Estimating thetas, neutrality test statistics=
			We also have working example for performing theta estimation.
			http://www.popgen.dk/angsd/index.php/Tajima#Example