sequencing/README.samtools_alignment at master · ccls/sequencing · GitHub

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Where does my read ACTCTCTG actually align?


If it aligns like so ...

         ACTCTCTG
         ||||||||
---------ACTCTCTG---
12345678901234567890


And you want to know the FIRST position of your read (say the beginning of an insertion)

samtools will say it aligned FORWARD at position 10 and this is the actual position.


If you wanted to know the LAST position of your read (say the ending of an insertion)

samtools will still say it aligned forward at position 10
but you would need to add the length minus 1 to get the location of G.


If it aligns REVERSE COMPLEMENTED like so ...

         CAGAGAGT
         ||||||||
---------CAGAGAGT---
12345678901234567890


And you want to know the FIRST position of your read (say the beginning of an insertion)

samtools will say it aligned REVERSE COMPLEMENTED at position 10

The actual position of the beginning of your read is
this position plus the length minus 1.


If you wanted to know the LAST position of your read (say the ending of an insertion)

samtools will still say it aligned REVERSE COMPLEMENTED at position 10
and this is the actual position of the end of your read.