Entering edit mode
5.1 years ago
BioinformaticsLad
▴
200
I ran reformat.sh on a SAM file and the log seemed fine:
Input is being processed as unpaired
Input: 35583 reads 52857642 bases
Output: 35583 reads (100.00%) 52857642 bases (100.00%)
But then in the results, the sum of the all matched bases across all Phred scores (95,085,736bp) exceeds the total number of bases aligned in my SAM file (52,857,642bp).
#Quality Match Sub Ins Del
0 0 0 0 0
1 0 0 0 0
… … … … …
40 2350122 634 2 14
41 92735614 15774 188 626
TOTAL 95085736 16408 190 640
So I was wondering how we're supposed to interpret these statistics?
I'm interested in quantifying the proportion of matched, mismatched, deleted and inserted bases from all my alignments. Is reformat.sh qahist the appropriate tool to use?
I hope Brian Bushnell sees this. I read through the BBMap documentation but couldn't find an explanation.