sambamba flagstat

Version:
0.6.x
Identifier: TL_bf790f_c2.e9

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Overview

Outputs some statistics drawn from read flags. First line contains numbers of QC-passed and QC-failed reads. Then come pairs of numbers, the former for QC-passed reads, the latter for QC-failed ones: duplicates mapped reads (plus percentage relative to the numbers from the first line) reads with 'is_paired' flag set paired reads which are first mates paired reads which are second mates paired reads with 'proper_pair' flag set (plus percentage relative to the numbers of QC-passed/failed reads with 'is_paired' flag set) paired reads where both mates are mapped paired reads where read itself is unmapped but mate is mapped paired reads where mate is mapped to a different chromosome the same as previous but mapping quality is not less than 5

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