Depth

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.