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 all -doCounts 1 -r 7: -nInd 5

Same as above but only using reads with a mapping quality above 30 and a nucleotide qscore above 20.

angsd -bam smallBam.filelist -doDepth 1 -out strict -doCounts 1 -r 7: -nInd 5 -minMapQ 30 -minQ 20

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.