ANGSD: Analysis of next generation Sequencing Data
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(Created page with "Depth -doDepth 1 -doCount 1 Prints the frequencies of depths for each individual to .depth file. Options - maxDepth [int] Defaults to 100. Sites with more than maxDepth ...") |
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Depth | =Depth= | ||
This method will find depth distribution for every sample and for all samples jointly. | |||
-doDepth 1 -doCount 1 | ;-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 | |||
<pre> | |||
angsd -bam smallBam.filelist -doDepth 1 -out CAN_DEL_ME -doCounts 1 -r 7: -nInd 5 | |||
</pre> | |||
==Output== | |||
Prints the frequencies of depths for each individual to .depth file. | Prints the frequencies of depths for each individual to .depth file. | ||
| Line 7: | Line 24: | ||
Options | Options | ||
Output | Output | ||
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 00:12, 12 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
Prints the frequencies of depths for each individual to .depth file.
Options
Output
The outputfile .depth has one line per individual, with maxDepth entries.