3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchUpdate rules used for creating the ASP
<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
== Rules ==
'''Dealing with 'N' Bases'''
* If the reference is 'N':
** Do Not write REF_ONLY or DETAILED records
** Either write EMPTY or no record (depending on Gap Size and the next data record)
* If all reads at this position are 'N':
** Either write EMPTY or no record (depending on Gap Size and the next data record)
* If some reads are 'N' and the rest are the reference (not 'N')
** Write a REF_ONLY record but do not include the 'N's in the numBases
* If some reads are 'N' and some are non-reference (not 'N')
** DEFAULT: Write a DETAILED record and include the 'N's in the numBases
** OPTIONAL: Write a DETAILED record but do not include the 'N's in the numBases
