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, 16:20, 28 October 2011
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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. |
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− | '''RESTRICTIONS'''
| + | = RESTRICTIONS = |
− | | |
− | This tool assumes the file is sorted by ReadName.
| |
| | | |
| + | *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 = |
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| | 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) |
| |} | | |} |
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| ! 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) |
| |} | | |} |
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