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Thorfinn: /* Bedfiles? */

2015-11-16T14:00:53Z

Bedfiles?

← Older revision		Revision as of 16:00, 16 November 2015
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	<pre>		<pre>
	awk '{print $1"\t"$2+1"\t"$3} input.bed >angsd.file		awk '{print $1"\t"$2+1"\t"$3}' input.bed >angsd.file
	</pre>		</pre>

2014-11-04T18:38:55Z

Bedfiles?

← Older revision		Revision as of 20:38, 4 November 2014
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	Bedfiles are chr pos1 pos2 value, and are zero indexed. Furthermore pos1 is included, but pos2 is not included.		Bedfiles are chr pos1 pos2 value, and are zero indexed. Furthermore pos1 is included, but pos2 is not included.
	You can convert with		You can convert to angsd format with

	<pre>		<pre>
	awk '{print $1"\t"$2+1"\t"$3} input.bed >angsd.file		awk '{print $1"\t"$2+1"\t"$3} input.bed >angsd.file
	</pre>		</pre>

2014-11-04T18:37:55Z

Requirements

@@ Line 96: / Line 96: @@
 <pre>
 sort -k1 unsorted.txt >sorted.txt
 </pre>

2014-11-04T11:04:31Z

Requirements

@@ Line 96: / Line 96: @@
 <pre>
 sort -k1 unsorted.txt >sorted.txt
 </pre>

2014-11-04T11:04:15Z

Internal representation

← Older revision		Revision as of 13:04, 4 November 2014
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	# filter.txt.bin		# filter.txt.bin
	# filter.txt.idx		# filter.txt.idx

			These can be printed using the command
			<pre>
			angsd sites print filter.txt
			</pre>

	=Requirements=		=Requirements=

2014-11-04T11:03:10Z

Example of filter file for single sites

← Older revision		Revision as of 13:03, 4 November 2014
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	chr1 2500000		chr1 2500000
	chr1 347348		chr1 347348
			</pre>
			==Example of filter file for regions==
			Example of a filter file.
			<pre>
			chr1 100 220
			chr1 1234 2234
			chr1 1000000 2000000
	</pre>		</pre>

2014-11-04T11:02:27Z

Example of filterfile

← Older revision		Revision as of 13:02, 4 November 2014
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	angsd sites index filename		angsd sites index filename
	</pre>		</pre>
	==Example of ~~filterfile~~==		==Example of filter file for single sites==
	Example of a filter file~~. File must be tab seperated~~.		Example of a filter file.
	<pre>		<pre>
	chr1 100001		chr1 100001
Line 57:		Line 57:
	chr1 347348		chr1 347348
	</pre>		</pre>


	==Example of augmented filterfile==		==Example of augmented filterfile==

2014-11-04T11:02:00Z

Details

← Older revision		Revision as of 13:02, 4 November 2014
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	-sites filename		-sites filename
	</pre>		</pre>
			And this file should be indexed before hand

			<pre>
			angsd sites index filename
			</pre>
	==Example of filterfile==		==Example of filterfile==
	Example of a filter file. File must be tab seperated.		Example of a filter file. File must be tab seperated.

2014-11-04T10:55:07Z

Details

← Older revision		Revision as of 12:55, 4 November 2014
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	We support 2 different kinds of inputfiles for filtering.		We support 3 different kinds of inputfiles for filtering.

	# Either the user supply a file containing chromsome and positions		# Either the user supply a file containing chromsome and positions
	# Or ~~the user~~ supply a file containing chromosome,position, major and minor		# Or supply regions like chr tab regStart tab regSTop
			# Or supply a file containing chromosome,position, major and minor

	Only sites contained in the filter file will be outputted. If you supply an augmented filter for the purpose of forcing a major and minor state then remember to supply '-doMajorMinor 3'		Only sites contained in the filter file will be outputted. If you supply an augmented filter for the purpose of forcing a major and minor state then remember to supply '-doMajorMinor 3'

2014-11-04T10:48:21Z

Brief overview

← Older revision		Revision as of 12:48, 4 November 2014
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	1) You can force major/minor by -doMajorMinor 3		1) You can force major/minor by -doMajorMinor 3
	And make sure file contains 4 columns (chr tab pos tab major tab minor)		And make sure file contains 4 columns (chr tab pos tab major tab minor)
			</pre>
			The -sites file is a nice ascii text file. ANGSD requires that a binary index version is generated. This is done by
			<pre>
			angsd sites index your.file
	</pre>		</pre>