HWE test - Revision history

Thorfinn: /* example */

2017-10-23T13:32:43Z

example

← Older revision		Revision as of 15:32, 23 October 2017
Line 29:		Line 29:
	most of the time it only makes sense to do for the variable site e.g.		most of the time it only makes sense to do for the variable site e.g.
	<pre>		<pre>
	angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1 -doMaf 1 SNP_pval 1e-6		angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1 -doMaf 1 -SNP_pval 1e-6
	</pre>		</pre>

Albrecht: /* options */

2017-07-18T13:38:28Z

options

← Older revision		Revision as of 15:38, 18 July 2017
Line 16:		Line 16:

	;-minHWEpval [float]		;-minHWEpval [float]
	Remove sites with a pvalue below this threshold. ~~E.i~~. only use with that does not violate HWE		Remove sites with a pvalue below this threshold i.e. only use with that does not violate HWE

	;-maxHWEpval [float]		;-maxHWEpval [float]

Albrecht at 13:38, 18 July 2017

2017-07-18T13:38:08Z

← Older revision		Revision as of 15:38, 18 July 2017
Line 15:		Line 15:
	Method only works for diallelic sites. There choose a methods for selecting the major and minor allele (see [[Inferring_Major_and_Minor_alleles]])		Method only works for diallelic sites. There choose a methods for selecting the major and minor allele (see [[Inferring_Major_and_Minor_alleles]])

			;-minHWEpval [float]
			Remove sites with a pvalue below this threshold. E.i. only use with that does not violate HWE

			;-maxHWEpval [float]
			Remove sites with a pvalue above this threshold. E.g. -maxHWEpval 1e-3 print only sites that violates HWE with a pvalue of less than 0.001

	==example==		==example==
Line 29:		Line 34:
	==Use as a filter==		==Use as a filter==

	see [[snpFilters]]		see [[snpFilters]], -minHWEpval or -maxHWEpval

	==Output==		==Output==

Albrecht: /* example */

2017-07-18T13:10:38Z

example

← Older revision		Revision as of 15:10, 18 July 2017
Line 24:		Line 24:
	most of the time it only makes sense to do for the variable site e.g.		most of the time it only makes sense to do for the variable site e.g.
	<pre>		<pre>
	angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1 --doMaf 1 SNP_pval 1e-6		angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1 -doMaf 1 SNP_pval 1e-6
	</pre>		</pre>

Albrecht: /* example */

2017-07-18T13:08:05Z

example

← Older revision		Revision as of 15:08, 18 July 2017
Line 20:		Line 20:
	<pre>		<pre>
	angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1		angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1
			</pre>

			most of the time it only makes sense to do for the variable site e.g.
			<pre>
			angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1 --doMaf 1 SNP_pval 1e-6
	</pre>		</pre>

Albrecht: /* Use as a filter */

2017-07-18T12:51:17Z

Use as a filter

← Older revision		Revision as of 14:51, 18 July 2017
Line 25:		Line 25:
	==Use as a filter==		==Use as a filter==

	see [snpFilters]		see [[snpFilters]]

	==Output==		==Output==

Albrecht at 12:50, 18 July 2017

2017-07-18T12:50:55Z

← Older revision		Revision as of 14:50, 18 July 2017
Line 6:		Line 6:

	If you want to estimate inbreeding for individuals or include inbreeding information in your analysis try [[HWE_and_Inbreeding_estimates]].		If you want to estimate inbreeding for individuals or include inbreeding information in your analysis try [[HWE_and_Inbreeding_estimates]].

			==options==

	;-doHWE [int]		;-doHWE [int]

Albrecht at 12:50, 18 July 2017

2017-07-18T12:50:13Z

← Older revision		Revision as of 14:50, 18 July 2017
Line 1:		Line 1:
	Test for Hardy Weinberg equilibrium based on genotype likelihoods. This class works both as a filter for all other classes and outputs the results in a file.		Test for Hardy Weinberg equilibrium based on genotype likelihoods. This class works both as a filter for all other classes and outputs the results in a file.

	~~The output described below are in the latest version of angsd run as default with the -doSnpStat 1, command.~~


Line 9:		Line 7:
	If you want to estimate inbreeding for individuals or include inbreeding information in your analysis try [[HWE_and_Inbreeding_estimates]].		If you want to estimate inbreeding for individuals or include inbreeding information in your analysis try [[HWE_and_Inbreeding_estimates]].

	;-~~HWE_pval~~ [~~float~~]		;-doHWE [int]
	~~p-value threshold. The value must be above 0 and a maximum of 1.~~		Estimate the divination from HWE for each site

	;-doMajorMinor [int]		;-doMajorMinor [int]
	Method only works for diallelic sites. There choose a methods for selecting the major and minor allele (see [[Inferring_Major_and_Minor_alleles]])		Method only works for diallelic sites. There choose a methods for selecting the major and minor allele (see [[Inferring_Major_and_Minor_alleles]])


			==example==

			<pre>
			angsd -bam bam.filelist -doHWE 1 -domajorminor 1 -GL 1

			</pre>

	==Use as a filter==		==Use as a filter==

	~~Sites with a p-value below the p-value threshold will be removed.~~		see [snpFilters]

	==Output==		==Output==

	This function will also print the results of the selected sites~~. If you choose -HWE_pval 1 then all sites (that pass other filters) will be outputted~~.		This function will also print the results of the selected sites.
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Example of output *.hwe.gz		Example of output *.hwe.gz

Thorfinn at 11:44, 15 December 2016

2016-12-15T11:44:36Z

@@ Line 9: / Line 9: @@
 If you want to estimate inbreeding for individuals or include inbreeding information in your analysis try [[HWE_and_Inbreeding_estimates]].
 ;-HWE_pval [float]
 p-value threshold. The value must be above 0 and a maximum of 1.

Thorfinn at 17:53, 24 November 2016

2016-11-24T17:53:58Z

← Older revision		Revision as of 19:53, 24 November 2016
Line 1:		Line 1:
	Test for Hardy Weinberg equilibrium based on genotype likelihoods. This class works both as a filter for all other classes and outputs the results in a file.		Test for Hardy Weinberg equilibrium based on genotype likelihoods. This class works both as a filter for all other classes and outputs the results in a file.

			The output described below are in the latest version of angsd run as default with the -doSnpStat 1, command.