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The <code>clipOverlap</code> option on the [[bamUtil]] executable clips overlapping read pairs.
The <code>clipOverlap</code> option on the [[bamUtil]] executable clips overlapping read pairs.
= RESTRICTIONS =
*Assumes the file is sorted by ReadName
*Assumes only 2 reads have matching ReadNames
**It matches in pairs, so if there are 3, the first 2 will be matched and compared, but the 3rd won't. If there are 4, the first 2 will be matched and the last 2 will be matched and compared.
*Only mapped reads will be clipped
= Rules for Clipping =
= Rules for Clipping =
| Removes the pad
| Removes the pad
|-
|-
| Last match/mismatch position of the read (the entire read is clipped)
| Clip occurs at the last match/mismatch position of the read (the entire read is clipped)
| Entire read is soft clipped, 0-based position changed left as the original (not modified)
| Entire read is soft clipped, 0-based position is left as the original (not modified)
|}
|}
! Clip Location !! How it is handled
! Clip Location !! How it is handled
|-
|-
|If the clip position falls in a skip/deletion
| Removes the entire skip/deletion
|-
|If the position immediately before the clip is a deletion/skip/pad
| Remove the deletion/skip/pad
|-
|If the position immediately before the clip is an insertion
| Leave the insertion, even if it results in a 70M3I27S
|-
|Clip occurs at the first position of the read (the entire read is clipped)
| Entire read is soft clipped, 0-based position is left as the original (not modified)
|}
|}
