294
edits
Changes
BWA
,no edit summary
== XT:A tag ==
N stands for for <tt>BWA_TYPE_NO_MATCH</tt> (bwtaln.h).If the number of ambiguous bases in the reference (XN:i tag) is greater than 10, this tag is also set to N. == NM, CM tags == If "-c" was given on the command line, CM is written and NM otherwise (the tags are mutually exclusive).
== XC:i tag ==
The XC:i tag is output when the clipped length of a read is less than the full read length.
== XO, XG tags ==
Documentation says that XG is the number gap extensions.
The source code seems to indicate that XG is the total no. of gaps (open+extend) (bwase.c):
printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
{{Link box}}
