ANGSD: Analysis of next generation Sequencing Data
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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 | ||
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;.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 | -.depthGlobal | ||
The sequencing depth for all samples. | |||
Revision as of 23:18, 11 October 2012
Depth
This method will find depth distribution for every sample and for all samples jointly.
- -doDepth 1
which requires -doCount 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 smallBam.filelist
angsd -bam smallBam.filelist -doDepth 1 -out CAN_DEL_ME -doCounts 1 -r 7: -nInd 5
Output
#.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
#.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
- .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.