ANGSD: Analysis of next generation Sequencing Data
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| Line 4: | Line 4: | ||
;-doDepth 1 | ;-doDepth 1 | ||
which requires - | which requires -doCounts 1. | ||
==Options== | ==Options== | ||
;- maxDepth [int] | ;- maxDepth [int] | ||
| Line 12: | Line 12: | ||
==Example== | ==Example== | ||
Find the depth for chromsome 7 for the first 5 samples in | Find the depth for chromsome 7 for the first 5 samples in bam.filelist | ||
<pre> | <pre> | ||
angsd -bam | 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. | |||
<pre> | |||
angsd -bam bam.filelist -doDepth 1 -out strict -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20 | |||
</pre> | |||
==Output== | ==Output== | ||
;.depthSample | |||
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 | |||
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 | ||
| Line 28: | Line 39: | ||
</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> | ||
<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> | |||
Latest revision as of 12:16, 3 January 2014
Depth
This method will find depth distribution for every sample and for all samples jointly.
- -doDepth 1
which requires -doCounts 1.
Options
- - maxDepth [int]
Defaults to 100. Sites with more than maxDepth reads are counted as having 100 reads.
Example
Find the depth for chromsome 7 for the first 5 samples in bam.filelist
angsd -bam bam.filelist -doDepth 1 -out all -doCounts 1 -r 7: -nInd 5
Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20.
angsd -bam bam.filelist -doDepth 1 -out strict -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20
Output
- .depthSample
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
The sequencing depth for all samples.
Here are the results the all data
#all.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 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 13131 24070 25347 18949 10514 5090 1991 688 213 82 21 0 0 0 0 0 0 0 0 0 0 0 0
#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
#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
#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