Allele Counts - Revision history

Thorfinn: /* Depth Distribution */

2020-05-02T04:34:54Z

Depth Distribution

← Older revision		Revision as of 06:34, 2 May 2020
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	==Depth Distribution==		==Depth Distribution==
	Column1 in the '''.depthSample,.depthGlobal''' contains the number of sites with sequencing depth of 1. Column2 is the number of sites with a sequencing depth of 2, etc.		Column1 in the '''.depthSample,.depthGlobal''' contains the number of sites with sequencing depth of 0. Column2 is the number of sites with a sequencing depth of 1, etc.

	The '''.depthSample''' contains depth per sample. Line one corresponds to individual 1. Column2 corresponds to individual 2 etc.		The '''.depthSample''' contains depth per sample. Line one corresponds to individual 1. Column2 corresponds to individual 2 etc.

Albrecht at 12:17, 26 February 2014

2014-02-26T12:17:40Z

← Older revision		Revision as of 14:17, 26 February 2014
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	You can refine which bases to be included using the filter parameters '''-minMapQ/-minQ/-trim'''. Based on the total depth for each you can discard sites for further analysis if the total depth is below/above some threshold '''-setMaxDepth/setMinDepth''', and you can discard a site if the effective sample size is below some threshold '''-minInd'''.		You can refine which bases to be included using the filter parameters '''-minMapQ/-minQ/-trim'''. Based on the total depth for each you can discard sites for further analysis if the total depth is below/above some threshold '''-setMaxDepth/setMinDepth''', and you can discard a site if the effective sample size is below some threshold '''-minInd'''.

	You can ~~dump~~ summary statistics such as ~~qscore~~ distribution '''-doQsDist''', depth distribution '''-doDepth''', or various per site counts '''-dumpCounts'''. All output files has a nice header which should make the interpretation straightforward.		You can output summary statistics such as Q score distribution '''-doQsDist''', depth distribution '''-doDepth''', or various per site counts '''-dumpCounts'''. All output files has a nice header which should make the interpretation straightforward.

	=Brief Overview=		=Brief Overview=
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	;-minQ [int]		;-minQ [int]
	Default 13, Discard bases with a qscore below this threshold.		Default 13, Discard bases with a qscore below this threshold.
	;-trim [0]		;-trim [int]
	Default 0. Trim ends of the reads. Useful for ~~aDNA~~.		Default 0. Trim [int] bases at both ends of the reads. Useful for ancient DNA.
	;-setMinDepth		;-setMinDepth [int]
	Default -1. If the total depth is below this value, ~~then discard~~ the site ~~for all analysis.~~		Default -1. If the total depth is below this value, the site is discarded
	;-setMaxDepth		;-setMaxDepth [int]
	Default -1. If the total depth is above this value, ~~then discard~~ the site ~~for all analysis.~~		Default -1. If the total depth is above this value, the site is discarded
	;-minQfile		;-minQfile [fileName]
	Default NULL. File with individual base quality score. This should be a file with the number of rows matching the number of individuals and the number of columns ~~shouls~~ either be 1 or 4. If four columns are given then a ~~seperate~~ quality threshold is used for each base (A C G T). Both space and tab is acceptable as delimiters.		Default NULL. File with individual base quality score. This should be a file with the number of rows matching the number of individuals and the number of columns should either be 1 or 4. If four columns are given then a separate quality threshold is used for each base (A C G T). Both space and tab is acceptable as delimiters.

	==~~File dumping~~==		==output summary==

	; -dumpCounts [int]		; -dumpCounts [int]
	Default 0. See examples below. Output files are called '''.pos,.counts.gz'''.		Default 0. See examples below. Output files are called '''.pos,.counts.gz'''.
	; -doQsDist [int]		; -doQsDist [int]
	Default 0. ~~Dump~~ the distribution of scores. Output files are called '''.qs'''.		Default 0. Output the distribution of scores. Output files are called '''.qs'''.
	; -doDepth [int]		; -doDepth [int]
	Default 0. ~~Dump~~ the distribution of sequencing depths. Sites with depth above> '''-maxDepth''', will be binned. Output files are called '''.depthSample,depthGlobal''''.		Default 0. Output the distribution of sequencing depths. Sites with depth above> '''-maxDepth''', will be binned. Output files are called '''.depthSample,depthGlobal''''.
	;-maxDepth [int]		;-maxDepth [int]
	Default 100. See '''-doDepth''' parameter.		Default 100. See '''-doDepth''' parameter.
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	30 34 34 30		30 34 34 30
	30 34 34 30		30 34 34 30
	~~30 34 34 30~~
	30 34 34 30		30 34 34 30
	~~...~~		30 34 34 30
			20 23 23 20
			30 34 34 30
			30 34 34 30
			20 30 30 20
			20 23 23 20
	</pre>		</pre>
	The above analysis removes A and T ~~based~~ with a q score less then 20 for individual 1. ~~Where as the~~ other individuals uses ~~a threshold og 30 for A and T but uses a the threshold of 34 for C and T~~		The above analysis removes A and T bases with a Q score less then 20 for individual 1. The other individuals uses different thresholds

	==qscore Distribution==		==qscore Distribution==

Albrecht: /* Example */

2013-12-04T12:40:11Z

Example

@@ Line 126: / Line 126: @@
 ./angsd -out out -doCounts 1 -dumpCounts 2 -bam bam.filelist
 </pre>
 ==qscore Distribution==

Albrecht: /* Filtering */

2013-12-04T12:32:23Z

Filtering

← Older revision		Revision as of 14:32, 4 December 2013
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	;-setMaxDepth		;-setMaxDepth
	Default -1. If the total depth is above this value, then discard the site for all analysis.		Default -1. If the total depth is above this value, then discard the site for all analysis.
			;-minQfile
			Default NULL. File with individual base quality score. This should be a file with the number of rows matching the number of individuals and the number of columns shouls either be 1 or 4. If four columns are given then a seperate quality threshold is used for each base (A C G T). Both space and tab is acceptable as delimiters.

	==File dumping==		==File dumping==

Albrecht: /* Brief Overview */

2013-12-04T12:27:38Z

Brief Overview

← Older revision		Revision as of 14:27, 4 December 2013
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	<pre>		<pre>
	./angsd -doCounts		./angsd -doCounts
	-> angsd version: 0.560 build(~~Nov 28~~ 2013 16:47:03)		-> angsd version: 0.560 build(Dec 4 2013 13:27:02)
	-> Analysis helpbox/synopsis information:		-> Analysis helpbox/synopsis information:
	---------------		---------------
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	-doCounts 0 (Count the number A,C,G,T. All sites, All samples)		-doCounts 0 (Count the number A,C,G,T. All sites, All samples)
	-minQ 13 (remove bases with qscore<minQ)		-minQ 13 (remove bases with qscore<minQ)
			-minQfile (null) file with individuals quality score threshold)
	-setMaxDepth -1 (If total depth is larger then site is removed from analysis.		-setMaxDepth -1 (If total depth is larger then site is removed from analysis.
	-1 indicates no filtering)		-1 indicates no filtering)

Thorfinn: /* Example */

2013-11-29T14:50:20Z

Example

← Older revision		Revision as of 16:50, 29 November 2013
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	0 1 0 0 0 0 0 0 0 0 0 0		0 1 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>
	==Example==		===Example===
	Print the individuals depth from bam files		Print the individuals depth from bam files
	<pre>		<pre>

Thorfinn: /* Printing Counts per site */

2013-11-29T14:50:01Z

Printing Counts per site

← Older revision		Revision as of 16:50, 29 November 2013
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	0 1 0 0 0 0 0 0 0 0 0 0		0 1 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>
			==Example==
			Print the individuals depth from bam files
			<pre>
			./angsd -out out -doCounts 1 -dumpCounts 2 -bam bam.filelist
			</pre>

	==qscore Distribution==		==qscore Distribution==
	Column 1 is the qscore value, and column 2 are the corresponding count.		Column 1 is the qscore value, and column 2 are the corresponding count.

Thorfinn: /* Example */

2013-11-29T14:49:47Z

Example

← Older revision		Revision as of 16:49, 29 November 2013
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	0 1 0 0 0 0 0 0 0 0 0 0		0 1 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>
	~~==Example==~~
	~~Print the individuals depth from bam files~~
	~~<pre>~~
	~~./angsd -out out -doCounts 1 -dumpCounts 2 -bam bam.filelist~~
	~~</pre>~~

	==qscore Distribution==		==qscore Distribution==
	Column 1 is the qscore value, and column 2 are the corresponding count.		Column 1 is the qscore value, and column 2 are the corresponding count.

Thorfinn: /* qscore Distribution */

2013-11-29T14:48:48Z

qscore Distribution

← Older revision		Revision as of 16:48, 29 November 2013
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	</pre>		</pre>

	=qscore Distribution=		==qscore Distribution==
	Column 1 is the qscore value, and column 2 are the corresponding count.		Column 1 is the qscore value, and column 2 are the corresponding count.
	<pre>		<pre>

Thorfinn: /* Depth Distribution */

2013-11-29T14:48:36Z

Depth Distribution

← Older revision		Revision as of 16:48, 29 November 2013
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	</pre>		</pre>

	=Depth Distribution=		==Depth Distribution==
	Column1 in the '''.depthSample,.depthGlobal''' contains the number of sites with sequencing depth of 1. Column2 is the number of sites with a sequencing depth of 2, etc.		Column1 in the '''.depthSample,.depthGlobal''' contains the number of sites with sequencing depth of 1. Column2 is the number of sites with a sequencing depth of 2, etc.