Allele Counts

Sometimes we want or need the frequency of the different bases. This is what -doCounts does.

You can refine which bases to be included using the filter parameters -minMapQ/-minQ/-trim. Bases on the total depth for each you can discard sites for further analysis if the total depth is below/above some threshold -setMaxDepth/setMinDepth, and you can discard a site if the effective sample size is below some threshold -minInd.

You can dump summary statistics such as qscore distribution -doQsDist, depth distribution -doDepth, or various per site counts -dumpCounts

Brief Overview

./angsd -doCounts 
	-> angsd version: 0.560	 build(Nov 28 2013 16:47:03)
	-> Analysis helpbox/synopsis information:
---------------
analysisCount.cpp:
	-doCounts	0	(Count the number A,C,G,T. All sites, All samples)
	-minQ		13	(remove bases with qscore<minQ)
	-setMaxDepth	-1	(If total depth is larger then site is removed from analysis.
				 -1 indicates no filtering)
	-setMinDepth	-1	(If total depth is smaller then site is removed from analysis.
				 -1 indicates no filtering)
	-trim		0	(trim ends of reads)
	-minInd		0	(Discard site if effective sample size below value.
				 0 indicates no filtering)
Filedumping:
	-doDepth	0	(dump distribution of seqdepth)	.depthSample,.depthGlobal
	  -maxDepth	100	(bin together high depths)
	-doQsDist	0	(dump distribution of qscores)	.qs
	-dumpCounts	0
	  1: total seqdepth for site	.pos.gz
	  2: seqdepth persample		.pos.gz,.counts.gz
	  3: A,C,G,T sum all samples	.pos.gz,.counts.gz
	  4: A,C,G,T sum every sample	.pos.gz,.counts.gz

Options

-dumpCounts [int]

see below

-minQ [int]

default 13. The minimum allowed base quality score.

-minInd [int]

default 0. Remove sites were less than 'minInd' individuals have at least one read.

printing counts

-dumpCounts [int]

1: print overall depth in the .pos file. This depth is the sum of reads covering a sites for all individuals. The first colum is the chromosome, the second it the position the third is the total depth

1	13999959	3
1	13999960	3
1	13999961	3
1	13999962	3
1	13999963	4
1	13999964	5
1	13999965	6
1	13999966	6
1	13999967	6
1	13999968	6

2: prints the depth of each individual. Example of the depth of 10 individuals. Each line corresponce to the same line in the postion file.

0	0	0	0	0	0	0	1	0	2
0	0	0	0	0	0	0	1	0	2
0	0	0	0	0	0	0	1	0	2
0	0	0	0	0	0	0	1	0	2
0	0	0	0	0	0	0	1	0	3
0	0	0	0	0	1	0	1	0	3
1	0	0	0	0	1	0	1	0	3
1	0	0	0	0	1	0	1	0	3
1	0	0	0	0	1	0	1	0	3
1	0	0	0	0	1	0	1	0	3

3: Prints the depth for each of the four bases for each indivial for each site. Example with the first four column belonging to the first individuals the counts of the number of A C G and Ts. Only two indivduals are shown. Each line corresponce to the same line in the postion file.

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	1	0	0	0	0	0	0	...
0	0	1	0	0	0	0	0	...
1	0	0	0	0	0	0	0	...
0	0	1	0	0	0	0	0	...

requred

In order to print the counts the options '-doCounts' have to be used and the input data needs to be sequence data.

Example

Print the individuals depth from bam files

./angsd -out out -doCounts 1 -dumpCounts 2 -bam bam.filelist