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* more README work
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iontorrent-dev committed Feb 16, 2012
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Expand Up @@ -3,7 +3,9 @@ The official SAMtools repository can be found at: http://samtools.sourceforge.ne

## Major fixes:
- added "samtools sample" command, to sample reads from a SAM/BAM file at a given frequency.
- added "samtools qa" command, to compute the mean and median coverage, as well a histogram from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX. Furthermore, "other" information is also available in the output file, namely:
- added "samtools qa" command, to compute the mean and median coverage, as well a histogram
from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX.
Furthermore, "other" information is also available in the output file, namely:
- Total number of reads
- Total number of duplicates found and ignored (duplicates are "found" based on the sam flag and are ignored in the counting of coverage)
- Percentage of unmapped reads
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