Base quality - Revision history

Thorfinn: /* options */

2013-09-30T07:17:33Z

options

← Older revision		Revision as of 09:17, 30 September 2013
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	; -minQ [int]		; -minQ [int]
	default 0. The minimum allowed base quality score.		default 0. The minimum allowed base quality score.
	; -~~minKeepIndC~~ [int]		; -minInd [int]
	default 0. Remove sites were less than '~~minKeepIndC~~' individuals have at least one read		default 0. Remove sites were less than 'minInd' individuals have at least one read

	==Example==		==Example==

Albrecht: /* options */

2013-02-27T10:11:18Z

options

← Older revision		Revision as of 12:11, 27 February 2013
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	; -minQ [int]		; -minQ [int]
	default 0. The minimum allowed base quality score.		default 0. The minimum allowed base quality score.
	~~; -minMapQ [int]~~
	~~default 0. The minimum allowed mapping quality score.~~
	; -minKeepIndC [int]		; -minKeepIndC [int]
	default 0. Remove sites were less than 'minKeepIndC' individuals have at least one read		default 0. Remove sites were less than 'minKeepIndC' individuals have at least one read

Albrecht at 15:23, 19 September 2012

2012-09-19T15:23:26Z

← Older revision		Revision as of 17:23, 19 September 2012
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	~~Counts the number of bases for each quality score.~~

	; -doQsDist 1		; -doQsDist 1
			Counts the number of bases for each quality score. Need the -doCount option to be invoked
			==options==
			; -minQ [int]
			default 0. The minimum allowed base quality score.
			; -minMapQ [int]
			default 0. The minimum allowed mapping quality score.
			; -minKeepIndC [int]
			default 0. Remove sites were less than 'minKeepIndC' individuals have at least one read

	==Example==		==Example==

Albrecht: /* Example */

2012-09-19T15:22:20Z

Example

← Older revision		Revision as of 17:22, 19 September 2012
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	Counts the number of bases for each quality score.		Counts the number of bases for each quality score.

			; -doQsDist 1

	==Example==		==Example==

Albrecht at 15:21, 19 September 2012

2012-09-19T15:21:27Z

← Older revision		Revision as of 17:21, 19 September 2012
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	~~=Base quality counts=~~
	Counts the number of bases for each quality score.		Counts the number of bases for each quality score.

Albrecht at 15:20, 19 September 2012

2012-09-19T15:20:16Z

@@ Line 1: / Line 1: @@
 =Base quality counts=
-Counts the number of bases for each quality.
+Counts the number of bases for each quality score.
 ==Example==
-Print the individuals depth from bam files
+Print the number of
 <pre>
 ./angsd -out out -doCounts 1 -doQsDist 1 -bam bam.filelist
 </pre>

Albrecht: Created page with "=Base quality counts= Counts the number of bases for each quality. ==Example== Print the individuals depth from bam files

 ./angsd -out out -doCounts 1 -doQsDist 1 -ba..."

2012-09-19T15:11:45Z

Created page with "=Base quality counts= Counts the number of bases for each quality. ==Example== Print the individuals depth from bam files <pre> ./angsd -out out -doCounts 1 -doQsDist 1 -ba..."

New page

=Base quality counts=
Counts the number of bases for each quality.

==Example==
Print the individuals depth from bam files
<pre>
./angsd -out out -doCounts 1 -doQsDist 1 -bam bam.filelist
</pre>