Allele Counts

Sometimes we want or need the frequency of the different bases. This is what -doCounts does. Using the filters minMapQ/minQ it will count the number of A,C,G,T for each individual for each site.

Allele counts

-doCounts 1

Counts the number of observed base types for each individual for each site.

options

-dumpCounts [int]

see below

-minQ [int]

default 0. 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