ANGSD: Analysis of next generation Sequencing Data
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Base quality: Difference between revisions
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; -minQ [int] | ; -minQ [int] | ||
default 0. The minimum allowed base quality score. | default 0. The minimum allowed base quality score. | ||
; -minKeepIndC [int] | ; -minKeepIndC [int] | ||
default 0. Remove sites were less than 'minKeepIndC' individuals have at least one read | default 0. Remove sites were less than 'minKeepIndC' individuals have at least one read | ||
Revision as of 11:11, 27 February 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.
- -minKeepIndC [int]
default 0. Remove sites were less than 'minKeepIndC' 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 . . .