From Genome Analysis Wiki
Jump to: navigation, search


393 bytes added, 00:14, 13 May 2010
Optional flags
Besides conforming to SAM specification, Karma developed its own optional tags to  help evaluate mapping.
{| cellspacing="1" cellpadding="1" border="1" widthstyle="600width: 1034px; height: 291px;"
| XA
| ER
| Different kind of errors when mapping: ER:Z:no_match -&gt; UNSET_QUALITY<br>ER:Z:invalid_bases -&gt; INVALID_DATA (not used yet)<br>ER:Z:duplicates -&gt; EARLYSTOP_DUPLICATES ( early stop due to reaching max number of best matches, with all bases matched)<br>ER:Z:quality -&gt; EARLYSTOP_QUALITY (early stop due to reaching max posterior quality)<br>ER:Z:repeats -&gt; REPEAT_QUALITY (not used yet)<br> 
= Other test and check capabilities =

Navigation menu