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From Genome Analysis Wiki
→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 -> UNSET_QUALITY<br>ER:Z:invalid_bases -> INVALID_DATA (not used yet)<br>ER:Z:duplicates -> EARLYSTOP_DUPLICATES ( early stop due to reaching max number of best matches, with all bases matched)<br>ER:Z:quality -> EARLYSTOP_QUALITY (early stop due to reaching max posterior quality)<br>ER:Z:repeats -> REPEAT_QUALITY (not used yet)<br>
|}
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= Other test and check capabilities =
