Depth - Revision history

Albrecht at 11:16, 3 January 2014

2014-01-03T11:16:05Z

← Older revision		Revision as of 13:16, 3 January 2014
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	==Example==		==Example==
	Find the depth for chromsome 7 for the first 5 samples in ~~smallBam~~.filelist		Find the depth for chromsome 7 for the first 5 samples in bam.filelist
	<pre>		<pre>
	angsd -bam ~~smallBam~~.filelist -doDepth 1 -out all -doCounts 1 -r 7: -nInd 5		angsd -bam bam.filelist -doDepth 1 -out all -doCounts 1 -r 7: -nInd 5
	</pre>		</pre>

	Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20.		Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20.
	<pre>		<pre>
	angsd -bam ~~smallBam~~.filelist -doDepth 1 -out strict -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20		angsd -bam bam.filelist -doDepth 1 -out strict -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20
	</pre>		</pre>

Thorfinn: /* Depth */

2013-02-08T11:39:24Z

Depth

← Older revision		Revision as of 13:39, 8 February 2013
Line 4:		Line 4:
	;-doDepth 1		;-doDepth 1

	which requires -~~doCount~~ 1.		which requires -doCounts 1.
	==Options==		==Options==
	;- maxDepth [int]		;- maxDepth [int]

Albrecht: /* Output */

2013-01-29T17:17:21Z

Output

← Older revision		Revision as of 19:17, 29 January 2013
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	==Output==		==Output==
	;.depthSample		;.depthSample
	This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=1,Column2 is the number of sites that has sequencing depth=2 etc		This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=0,Column2 is the number of sites that has sequencing depth=1 etc

	;.depthGlobal		;.depthGlobal
	The sequencing depth for all samples.		The sequencing depth for all samples.

	Here are the results the all data		Here are the results the all data

Thorfinn: /* Output */

2012-10-11T22:23:54Z

Output

← Older revision		Revision as of 00:23, 12 October 2012
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	==Output==		==Output==
			;.depthSample
			This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=1,Column2 is the number of sites that has sequencing depth=2 etc

			;.depthGlobal
			The sequencing depth for all samples.

			Here are the results the all data
	<pre>		<pre>
	#.depthSample		#all.depthSample
	1147 4240 8357 13017 16077 15481 12871 10738 7288 4537 2998 1638 889 451 211 92 50 14		1147 4240 8357 13017 16077 15481 12871 10738 7288 4537 2998 1638 889 451 211 92 50 14
	1831 6725 12572 17090 17451 15359 11588 8274 4538 2551 1199 545 209 83 20 33 13 9		1831 6725 12572 17090 17451 15359 11588 8274 4538 2551 1199 545 209 83 20 33 13 9
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	</pre>		</pre>
	<pre>		<pre>
	#.depthGlobal		#all.depthGlobal
	150500 21708 39928 65820 87290 97337 105127 115961 123207 126721 129377 127351 125596 118588 107096 93171 78612 66905 53952 43224 34777 25672 19393 14431 9771 6958 4837 3149 2027 1362 919 471 308 198 79 48 41 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		150500 21708 39928 65820 87290 97337 105127 115961 123207 126721 129377 127351 125596 118588 107096 93171 78612 66905 53952 43224 34777 25672 19393 14431 9771 6958 4837 3149 2027 1362 919 471 308 198 79 48 41 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>
	~~;.depthSample~~
	~~This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=1,Column2 is the number of sites that has sequencing depth=2 etc~~

	;.depthGlobal
	~~The sequencing depth for all samples.~~		<pre>
			#strict.depthSample
			6391 11709 16031 17921 16209 12232 8424 5352 2913 1552 814 348 129 53 15 3 0 0 0
			7735 17432 20843 19832 14877 9459 5334 2679 1139 468 185 63 26 11 9 2 2 0 0 0 0
			25931 30865 23189 12260 5217 1860 579 152 35 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
			21104 29568 23802 13951 7090 3028 1157 327 52 16 1 0 0 0 0 0 0 0 0 0 0 0 0 0
			25971 30627 23572 12355 5041 1775 561 149 32 9 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0
			</pre>

			<pre>
			#strict.depthGlobal
			182709 73098 106362 134201 153550 161615 163108 161384 155021 139328 124616 106576 87303 68862 53696 40599 29287 20417 14767 9702 6299 3833 2415 1435 827 457 260 108 35 25 19 1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

			</pre>

Thorfinn: /* Example */

2012-10-11T22:21:38Z

Example

← Older revision		Revision as of 00:21, 12 October 2012
Line 17:		Line 17:
	</pre>		</pre>

	Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20		Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20.
	<pre>		<pre>
	angsd -bam smallBam.filelist -doDepth 1 -out ~~all~~ -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20		angsd -bam smallBam.filelist -doDepth 1 -out strict -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20
	</pre>		</pre>

Thorfinn: /* Example */

2012-10-11T22:21:19Z

Example

← Older revision		Revision as of 00:21, 12 October 2012
Line 14:		Line 14:
	Find the depth for chromsome 7 for the first 5 samples in smallBam.filelist		Find the depth for chromsome 7 for the first 5 samples in smallBam.filelist
	<pre>		<pre>
	angsd -bam smallBam.filelist -doDepth 1 -out ~~CAN_DEL_ME~~ -doCounts 1 -r 7: -nInd 5		angsd -bam smallBam.filelist -doDepth 1 -out all -doCounts 1 -r 7: -nInd 5
	</pre>		</pre>

			Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20
			<pre>
			angsd -bam smallBam.filelist -doDepth 1 -out all -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20
			</pre>

	==Output==		==Output==

Thorfinn: /* Output */

2012-10-11T22:18:46Z

Output

← Older revision		Revision as of 00:18, 12 October 2012
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	This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=1,Column2 is the number of sites that has sequencing depth=2 etc		This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=1,Column2 is the number of sites that has sequencing depth=2 etc

	-.depthGlobal		;.depthGlobal
	The sequencing depth for all samples.		The sequencing depth for all samples.

Thorfinn: /* Output */

2012-10-11T22:18:33Z

Output

← Older revision		Revision as of 00:18, 12 October 2012
Line 31:		Line 31:
	150500 21708 39928 65820 87290 97337 105127 115961 123207 126721 129377 127351 125596 118588 107096 93171 78612 66905 53952 43224 34777 25672 19393 14431 9771 6958 4837 3149 2027 1362 919 471 308 198 79 48 41 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		150500 21708 39928 65820 87290 97337 105127 115961 123207 126721 129377 127351 125596 118588 107096 93171 78612 66905 53952 43224 34777 25672 19393 14431 9771 6958 4837 3149 2027 1362 919 471 308 198 79 48 41 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>
			;.depthSample
			This file contains nInd number of lines. Column1 is the number sites that has sequencing depth=1,Column2 is the number of sites that has sequencing depth=2 etc

	The ~~outputfile .~~depth ~~has one line per individual, with maxDepth entries~~.		-.depthGlobal
			The sequencing depth for all samples.

Thorfinn: /* Output */

2012-10-11T22:16:34Z

Output

← Older revision		Revision as of 00:16, 12 October 2012
Line 20:		Line 20:
	==Output==		==Output==
	<pre>		<pre>
	1147 4240 8357 13017 16077 15481 12871 10738 7288 4537 2998 1638 889 451 211 92 50		#.depthSample
			1147 4240 8357 13017 16077 15481 12871 10738 7288 4537 2998 1638 889 451 211 92 50 14
	1831 6725 12572 17090 17451 15359 11588 8274 4538 2551 1199 545 209 83 20 33 13 9		1831 6725 12572 17090 17451 15359 11588 8274 4538 2551 1199 545 209 83 20 33 13 9
	12749 23974 25261 18900 10294 5388 2326 850 241 83 28 2 0 0 0 0 0 0 0 0 0 0 0		12749 23974 25261 18900 10294 5388 2326 850 241 83 28 2 0 0 0 0 0 0 0 0 0 0 0
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	13131 24070 25347 18949 10514 5090 1991 688 213 82 21 0 0 0 0 0 0 0 0 0 0 0 0		13131 24070 25347 18949 10514 5090 1991 688 213 82 21 0 0 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>
			<pre>
			#.depthGlobal
			150500 21708 39928 65820 87290 97337 105127 115961 123207 126721 129377 127351 125596 118588 107096 93171 78612 66905 53952 43224 34777 25672 19393 14431 9771 6958 4837 3149 2027 1362 919 471 308 198 79 48 41 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
			</pre>

	The outputfile .depth has one line per individual, with maxDepth entries.		The outputfile .depth has one line per individual, with maxDepth entries.

Thorfinn: /* Output */

2012-10-11T22:15:08Z

Output

← Older revision		Revision as of 00:15, 12 October 2012
Line 20:		Line 20:
	==Output==		==Output==
	<pre>		<pre>
	~~147~~ 4240 8357 13017 16077 15481 12871 10738 7288 4537 2998 1638 889 451 211 92 50 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		1147 4240 8357 13017 16077 15481 12871 10738 7288 4537 2998 1638 889 451 211 92 50
	1831 6725 12572 17090 17451 15359 11588 8274 4538 2551 1199 545 209 83 20 33 13 9 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		1831 6725 12572 17090 17451 15359 11588 8274 4538 2551 1199 545 209 83 20 33 13 9
	12749 23974 25261 18900 10294 5388 2326 850 241 83 28 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		12749 23974 25261 18900 10294 5388 2326 850 241 83 28 2 0 0 0 0 0 0 0 0 0 0 0
	15366 25983 24257 16854 9152 4832 2585 791 214 42 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		15366 25983 24257 16854 9152 4832 2585 791 214 42 20 0 0 0 0 0 0 0 0 0 0 0 0
	13131 24070 25347 18949 10514 5090 1991 688 213 82 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0		13131 24070 25347 18949 10514 5090 1991 688 213 82 21 0 0 0 0 0 0 0 0 0 0 0 0
	</pre>		</pre>


	The outputfile .depth has one line per individual, with maxDepth entries.		The outputfile .depth has one line per individual, with maxDepth entries.