ANGSD: Analysis of next generation Sequencing Data
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==Output== | ==Output== | ||
<pre> | <pre> | ||
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 | 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 | ||
15366 25983 24257 16854 9152 4832 2585 791 214 42 20 | 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 | 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. | ||
Revision as of 23:15, 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
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 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
The outputfile .depth has one line per individual, with maxDepth entries.