Changes

From Genome Analysis Wiki
Jump to navigationJump to search

BamUtil: asp (view source)

Revision as of 17:38, 3 January 2014

600 bytes removed ,  17:38, 3 January 2014
no edit summary
Line 7: Line 7:     
<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
      Line 32: Line 47:  
</pre>
 
</pre>
    +
== Required Parameters ==
 
{{inBAMInputFile}}
 
{{inBAMInputFile}}
   −
== output File <code>(--out)</code>==
+
=== output File <code>(--out)</code>===
    
Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup.
 
Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup.
Line 41: Line 57:     
{{RefFile}}
 
{{RefFile}}
 +
 +
== Optional Parameters ==
 
{{BamIndex}}
 
{{BamIndex}}
   −
== Region List <code>(--regionList)</code> ==  
+
=== Region List <code>(--regionList)</code> ===
 
Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file.  The region list file has one region on each line.
 
Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file.  The region list file has one region on each line.
   Line 56: Line 74:  
If a position is covered by multiple regions, the position will be piled up multiple times (once for each region).
 
If a position is covered by multiple regions, the position will be piled up multiple times (once for each region).
   −
== Gap Size <code>(--gapSize)</code> ==
+
=== Gap Size <code>(--gapSize)</code> ===
 
When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them.   
 
When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them.   
 
# Write an Empty record indicating no data for that position.
 
# Write an Empty record indicating no data for that position.
Line 68: Line 86:  
{{paramsParameter}}
 
{{paramsParameter}}
   −
  −
== Asp File Name <code>(--asp)</code>==
  −
  −
Use <code>--asp</code> followed by the file name of the ASP file that you want to read.
  −
  −
== Only print Data Records <code>(--dataOnly)</code>==
  −
The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records.  Any Empty and Position records are not printed.
  −
  −
{{paramsParameter}}
      
= Return Value =
 
= Return Value =
Line 83: Line 92:     
=Output=
 
=Output=
−
Each ASP record is printed on one line with each field separated by a <code>tab</code>.
+
An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file.  ASP files are by default compressed using BGZF.
   −
The 1st field in the row is the chromosomeID and 0-based position separated by a ':'.
+
The number of each type of record is output to stderr.
   −
The 2nd field is the record type, <code>POS</code>, <code>EMPTY</code>, <code>REF_ONLY</code>, or <code>DETAILED</code>.
+
For example:
−
 
+
<pre>
−
<code>POS</code> and <code>EMPTY</code> records have no additional columns.
+
Number of Position Records = 6
−
 
+
Number of Empty Records = 39
−
<code>REF_ONLY</code> records have 3 additional fields:
+
Number of Reference Only Records = 12
−
# numBases - the number of bases at this position
+
Number of Detailed Records = 29
−
# GLH - the GLH for this position
+
</pre>
−
# GLA - the GLA for this position
  −
 
  −
<code>DETAILED</code> records have 6 additional fields:
  −
# numBases - the number of bases at this position
  −
# bases - the bases at this position.  String of ACTGND characters that is numBases long.  ('D' represents a deletion)
  −
# qualities - the qualities at this position.  String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
  −
# cycles - the cycles for this position.  There are numBases cycles, separated by a ':'.  (-1 represents the cycle of a deletion)
  −
# strands - the strands for this position.  Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
  −
# mqs - the mapping qualities for this position.  There are numBases mapping qualities, separated by a ':'.
  −
 
  −
==Sample Output==
 
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/4388...9216"

Navigation menu