ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.918/0.919 on github), see Change_log for changes, and download it here.

Base quality

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-doQsDist 1

Counts the number of bases for each quality score. Need the -doCount option to be invoked

options

-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

Example

Print the number of

./angsd -out out -doCounts 1 -doQsDist 1 -bam bam.filelist

output

First coloums is the quality score the second one the number of bases with this score.

0       3113
1       15619
2       97044
3       68369
4       117163
5       12149
6       15016
7       17982
8       21897
9       26471
10      31854
11      36491
12      41649
13      47400
14      53778
15      61933
16      73120
17      87034
.
.
.