ANGSD: Analysis of next generation Sequencing Data
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Base quality: Difference between revisions
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(Created page with "=Base quality counts= Counts the number of bases for each quality. ==Example== Print the individuals depth from bam files <pre> ./angsd -out out -doCounts 1 -doQsDist 1 -ba...") |
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; -doQsDist 1 | |||
Counts the number of bases for each quality. | 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== | ==Example== | ||
Print the | Print the number of | ||
<pre> | <pre> | ||
./angsd -out out -doCounts 1 -doQsDist 1 -bam bam.filelist | ./angsd -out out -doCounts 1 -doQsDist 1 -bam bam.filelist | ||
</pre> | |||
===output=== | |||
First coloums is the quality score the second one the number of bases with this score. | |||
<pre> | |||
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 | |||
. | |||
. | |||
. | |||
</pre> | </pre> | ||
Latest revision as of 08:17, 30 September 2013
- -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 . . .