SnpFilters - Revision history

Thorfinn: /* Example run with hetfilter */

2017-06-27T19:24:23Z

Example run with hetfilter

← Older revision		Revision as of 21:24, 27 June 2017
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	1 14004623 57 21 56 34 -0.331562:0.410438:0.142272 0.621479:4.304982e-01 -1.788061:7.376604e-02 -1.226968:2.198347e-01 -0.655735:5.119945e-01 18 10 13 24 65 0.138462:7.098153e-01		1 14004623 57 21 56 34 -0.331562:0.410438:0.142272 0.621479:4.304982e-01 -1.788061:7.376604e-02 -1.226968:2.198347e-01 -0.655735:5.119945e-01 18 10 13 24 65 0.138462:7.098153e-01
	</pre>		</pre>
	~~output~~		The last columns are the counts of major/minor over +/- strand along with the test statistic and the corresponding pvalue.

	=Source Code=		=Source Code=

2017-06-27T19:22:30Z

Example run with hetfilter

← Older revision		Revision as of 21:22, 27 June 2017
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	</pre>		</pre>

			<pre>
	gunzip -c to.snpStat.gz \|head		gunzip -c to.snpStat.gz \|head
	Chromo Position +Major +Minor -Major -Minor SB1:SB2:SB3 HWE_LRT:HWE_pval baseQ_Z:baseQ_pval mapQ_Z:mapQ_pval edge_z:edge_pval +MajorHet +MinorHet -MajorHet -MinorHet nHet hetStat:hetStat_pval		Chromo Position +Major +Minor -Major -Minor SB1:SB2:SB3 HWE_LRT:HWE_pval baseQ_Z:baseQ_pval mapQ_Z:mapQ_pval edge_z:edge_pval +MajorHet +MinorHet -MajorHet -MinorHet nHet hetStat:hetStat_pval

2017-06-27T19:22:19Z

Example run with hetfilter

2017-06-27T19:22:10Z

Example run with hetfilter

@@ Line 60: / Line 60: @@
   ./angsd -dosnpstat 1 -b list -domajorminor 1 -gl 1 -snp_pval 1e-6 -domaf 1 -dogeno 3 -dopost 2 -out to -hetbias_pval 0.05
 </pre>
 =Source Code=

2017-06-27T19:21:11Z

Example run with hetfilter

← Older revision		Revision as of 21:21, 27 June 2017
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	=Example run with hetfilter=		=Example run with hetfilter=
			<pre>
			./angsd -dosnpstat 1 -b list -domajorminor 1 -gl 1 -snp_pval 1e-6 -domaf 1 -dogeno 3 -dopost 2 -out to -hetbias_pval 0.05
			</pre>

	=Source Code=		=Source Code=

2017-06-27T19:20:39Z

2017-06-27T19:05:41Z

← Older revision		Revision as of 21:05, 27 June 2017
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	;* deviation from HWE		;* deviation from HWE
	;* Wilcox rank sum test for qscore bias		;* Wilcox rank sum test for qscore bias
	* edge bias		;* edge bias
			;* hetbias filter (based on reads of the genotypes that are called to be heterozygotes. This therefore requires -doGeno option)

	The 3 strand bias filters are described here: http://www.biomedcentral.com/1471-2164/13/666		The 3 strand bias filters are described here: http://www.biomedcentral.com/1471-2164/13/666

2016-11-24T17:45:12Z

← Older revision		Revision as of 19:45, 24 November 2016
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	;* deviation from HWE		;* deviation from HWE
	;* Wilcox rank sum test for qscore bias		;* Wilcox rank sum test for qscore bias
			* edge bias


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	-edge_pval		-edge_pval
	</pre>		</pre>

			Sites with pvalue in the interval (0-cutoff) will be discarded.

	=Example Output=		=Example Output=

2016-11-24T17:43:18Z

← Older revision		Revision as of 19:43, 24 November 2016
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	</pre>		</pre>

	Please notice that '''-doSnpStat 1''' does not filter out sites, but will only report stats. In the above command we therefore limit the analysis and output to the sites that are likely to be truly variable (-snp_pval 1e-2). ~~But we calculate HWE deviations from all sites, but does not~~ filter by ~~it (~~-hwe_pval 1)		Please notice that '''-doSnpStat 1''' does not filter out sites, but will only report stats. In the above command we therefore limit the analysis and output to the sites that are likely to be truly variable (-snp_pval 1e-2).

			You filter by supply pvalue cutoffs.
			Some examples are
			<pre>
			-sb_pval
			-qscore_pval
			-hwe_pval
			-edge_pval
			</pre>

	=Example Output=		=Example Output=

2016-11-24T17:13:59Z

← Older revision		Revision as of 19:13, 24 November 2016
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	These statistics will be calculated and reported and written into a file called '''PREFIX.snpStat.gz'''		These statistics will be calculated and reported and written into a file called '''PREFIX.snpStat.gz'''

	~~The HWE requies -dohwe which is depended on domaf. So a full example would be:~~

	<pre>		<pre>