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

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.