Fasta - Revision history

Albrecht: /* Ancestral fasta using multiple outgroup */

2023-02-06T16:45:55Z

Ancestral fasta using multiple outgroup

← Older revision		Revision as of 18:45, 6 February 2023
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	=Ancestral fasta using multiple ~~outgroup~~=		=Ancestral fasta using multiple outgroups=
	If you have outgroup species map to your reference genome and you want to use them to make a fasta file with ancestral alleles. You can use one or more outgroup individuals e.g. for human you could have a four outgroup bam file from a chimp, a bonobo, a gorrilla and a orangotan. Assuming you want to make a fasta file where the alleles is the same for all outgroup species then you can use a command like		If you have outgroup species map to your reference genome and you want to use them to make a fasta file with ancestral alleles. You can use one or more outgroup individuals e.g. for human you could have a four outgroup bam file from a chimp, a bonobo, a gorrilla and a orangotan. Assuming you want to make a fasta file where the alleles is the same for all outgroup species then you can use a command like

2023-02-06T16:45:47Z

Ancestral fasta

← Older revision		Revision as of 18:45, 6 February 2023
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	=Ancestral fasta=		=Ancestral fasta using multiple outgroup=
	If you have outgroup species map to your reference genome and you want to use them to make a fasta file with ancestral alleles. You can use one or more outgroup individuals e.g. for human you could have a four outgroup bam file from a chimp, a bonobo, a gorrilla and a orangotan. Assuming you want to make a fasta file where the alleles is the same for all outgroup species then you can use a command like		If you have outgroup species map to your reference genome and you want to use them to make a fasta file with ancestral alleles. You can use one or more outgroup individuals e.g. for human you could have a four outgroup bam file from a chimp, a bonobo, a gorrilla and a orangotan. Assuming you want to make a fasta file where the alleles is the same for all outgroup species then you can use a command like

2023-02-06T16:44:52Z

Options

← Older revision		Revision as of 18:44, 6 February 2023
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	a fasta file used to determine if a site is a transitions (needed when using -rmTrans 1 is used)		a fasta file used to determine if a site is a transitions (needed when using -rmTrans 1 is used)
	;-seed [INT]		;-seed [INT]
	Use a seed in order to replicate results		Use a seed in order to replicate results ( relevant when using random sample -dofasta 1 )

	For filters see [[Filters]]		For filters see [[Filters]]

2023-02-06T16:43:52Z

Ancestral fasta

← Older revision		Revision as of 18:43, 6 February 2023
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	'''-b fourOutgroup.bamlist''' contains the bam files for four outgroup individuals.		'''-b fourOutgroup.bamlist''' contains the bam files for four outgroup individuals.


	'''-out myFasta''' the output name		'''-out myFasta''' the output name
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	'''-setMinDepthInd 10''' require at least 10 read for each individual		'''-setMinDepthInd 10''' require at least 10 read for each individual

			''' -explode 1''' make the fasta file for the whole genome not just the chromosomes/scaffolds were you have data

			The sites that are polymorphic or do not have enough data will be labeled as 'N' in the fasta file

2023-02-06T16:41:43Z

Ancestral fasta

← Older revision		Revision as of 18:41, 6 February 2023
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	</pre>		</pre>
	~~here~~ fourOutgroup.bamlist contains the bam files for four outgroup individuals.
			'''-b fourOutgroup.bamlist''' contains the bam files for four outgroup individuals.


			'''-out myFasta''' the output name

			'''-doCounts 1''' counts bases accross individuals to determine the concensus allele

			'''-snp_pval 0.01''' p-value threshold for defining a SNP. A lower threshold will need more evidence to call a SNPs.

			''' -domaf 1''' estimate allele frequency (use to call SNPs) with that the major and minor alleles inferred from data

			'''-domajorminor 1''' infer the major and minor allele from data

			'''-gl 2''' use genotype likelihoods based on the GATK model

			''' -rmSNPs 1''' remove polymorphic sites. instead of keeping sites that are polymorphic then we remove them such that all outgroups have the same allele.

			''' -minind 4''' remove site where you don't have data for all four individuals

			'''-setMinDepthInd 10''' require at least 10 read for each individual

2023-02-06T16:32:53Z

← Older revision		Revision as of 18:32, 6 February 2023
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	where <math>b</math> is a certain base, <math>N_b</math> is the number of reads with base <math>b</math>		where <math>b</math> is a certain base, <math>N_b</math> is the number of reads with base <math>b</math>


			=Ancestral fasta=
			If you have outgroup species map to your reference genome and you want to use them to make a fasta file with ancestral alleles. You can use one or more outgroup individuals e.g. for human you could have a four outgroup bam file from a chimp, a bonobo, a gorrilla and a orangotan. Assuming you want to make a fasta file where the alleles is the same for all outgroup species then you can use a command like

			<pre>
			./angsd -b fourOutgroup.bamlist -out myFasta -doCounts 1 -snp_pval 0.01 -domaf 1 -domajorminor 1 -gl 2 -rmSNPs 1 -minind 4 -setMinDepthInd 10 -explode 1

			</pre>
			here fourOutgroup.bamlist contains the bam files for four outgroup individuals.

2017-09-26T16:09:03Z

← Older revision		Revision as of 18:09, 26 September 2017
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	# [[ABBA-BABA]]		# [[ABBA-BABA]]

			The iupac output code was kindly provided by Kristian Ullrich.
	=Brief Overview=		=Brief Overview=
	<pre>		<pre>

2017-09-26T16:02:36Z

Brief Overview

← Older revision		Revision as of 18:02, 26 September 2017
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	=Brief Overview=		=Brief Overview=
	<pre>		<pre>
	./angsd -~~doFasta~~ -> ~~Wed Nov 16 16~~:58:~~52 2016~~		./angsd -dofasta -> Tue Sep 26 17:02:07 2017
	--------------		--------------
	abcWriteFasta.cpp:		abcWriteFasta.cpp:
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	2: use the most common (non N) base (needs -doCounts 1)		2: use the most common (non N) base (needs -doCounts 1)
	3: use the base with highest ebd (under development)		3: use the base with highest ebd (under development)
			4: output iupac codes (under development)
	-basesPerLine 50 (Number of bases perline in output file)		-basesPerLine 50 (Number of bases perline in output file)
	-explode 0 print chromosome where we have no data (0:no,1:yes)		-explode 0 print chromosome where we have no data (0:no,1:yes)
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	-ref (null) reference fasta, only used with -rmTrans 1		-ref (null) reference fasta, only used with -rmTrans 1
	-seed 0 use non random seed of value 1		-seed 0 use non random seed of value 1

	</pre>		</pre>

2017-09-26T16:01:56Z

← Older revision		Revision as of 18:01, 26 September 2017
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	<classdiagram type="dir:LR">		<classdiagram type="dir:LR">
	[Multiple BAM files{bg:orange}]->[Sequence data\|Random base (-doFasta 1);Consensus base (-doFasta 2)]		[Multiple BAM files{bg:orange}]->[Sequence data\|Random base (-doFasta 1);Consensus base (-doFasta 2);write iupac (-doFasta 4)]
	[sequence data]->doFasta[fasta file{bg:blue}]		[sequence data]->doFasta[fasta file{bg:blue}]
	</classdiagram>		</classdiagram>

2017-09-26T16:00:43Z

← Older revision		Revision as of 18:00, 26 September 2017
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	<classdiagram type="dir:LR">		<classdiagram type="dir:LR">
	[Single BAM file{bg:orange}]->[Sequence data\|Random base (-doFasta 1);Consensus base (-doFasta 2);Highest EBD (-doFasta 3)]		[Single BAM file{bg:orange}]->[Sequence data\|Random base (-doFasta 1);Consensus base (-doFasta 2);Highest EBD (-doFasta 3); write iupac (-doFasta 4)]
	[sequence data]->doFasta[fasta file{bg:blue}]		[sequence data]->doFasta[fasta file{bg:blue}]
	</classdiagram>		</classdiagram>