BamUtil: asp - Revision history

Mktrost at 21:38, 3 January 2014

2014-01-03T21:38:39Z

← Older revision		Revision as of 17:38, 3 January 2014
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	</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.
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	{{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.

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	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.

Mktrost at 19:40, 21 March 2012

2012-03-21T19:40:56Z

← Older revision		Revision as of 15:40, 21 March 2012
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	=Output=		=Output=
	An [[LibStatGen: ASP\|ASP]] file is written containing the pileup for the specified BAM file.		An [[LibStatGen: ASP\|ASP]] file is written containing the pileup for the specified BAM file. ASP files are by default compressed using BGZF.

			The number of each type of record is output to stderr.

			For example:
			<pre>
			Number of Position Records = 6
			Number of Empty Records = 39
			Number of Reference Only Records = 12
			Number of Detailed Records = 29
			</pre>

Mktrost: Update rules used for creating the ASP

2012-03-21T13:53:11Z

Update rules used for creating the ASP

← Older revision		Revision as of 09:53, 21 March 2012
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	<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

Mktrost at 21:08, 27 January 2012

2012-01-27T21:08:16Z

@@ Line 68: / Line 68: @@
 {{paramsParameter}}
 = Return Value =
@@ Line 83: / Line 74: @@
 =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.

Mktrost: Created page with 'asp Category:BAM Software Category:Software = Overview of the `asp` function of `bamUtil` = The `asp` option on the…'

2012-01-27T21:06:53Z

Created page with 'asp Category:BAM Software Category:Software = Overview of the <code>asp</code> function of <code>bamUtil</code> = The <code>asp</code> option on the…'

New page

[[Category:BamUtil|asp]]
[[Category:BAM Software]]
[[Category:Software]]

= Overview of the <code>asp</code> function of <code>bamUtil</code> =
The <code>asp</code> option on the [[bamUtil]] executable generates a pileup in [[LibStatGen: ASP|ASP]] format from the specified BAM file.

<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>

= Usage =
./bam asp --in <inputFile> --out <outputFile> --refFile <referenceFilename> [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--noeof] [--params]

= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to calculate asp for
--out : the output file to write
--refFile : the reference file
Optional Parameters:
--bamIndex : The path/name of the bam index file
(if required and not specified uses the --in value + ".bai")
--regionList : File containing the regions to be processed chr<tab>start_pos<tab>end<pos>.
Positions are 0 based and the end_pos is not included in the region.
Uses bamIndex.
--gapSize : Gap Size threshold such that position gaps less than this size have an
empty record written, while gaps larger than this size have a new
chrom/position header written, Default = 100.
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings
</pre>

{{inBAMInputFile}}

== output File <code>(--out)</code>==

Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup.

To compress the output, specify a filename with a .gz extension.

{{RefFile}}
{{BamIndex}}

== 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.

Format of each line:
<pre>
chr<tab>start_pos<tab>end<pos>
</pre>
The positions are 0 based and the end_pos is not included in the region.

This option uses a bamIndex file for jumping between the regions.

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> ==
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 a new position record indicating the next position that has data.

The <code>--gapSize</code> option specifies at what point a Position record should be written instead of an Empty record. If the space between two positions that have data is larger than the gap size, then a Position record is written. Otherwise Empty records are written until the next position that has data.

The default gap size is 100.

{{noeofBGZFParameter}}
{{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 =
* 0: the file was processed successfully.
* non-0: the file was not processed successfully.

=Output=
Each ASP record is printed on one line with each field separated by a <code>tab</code>.

The 1st field in the row is the chromosomeID and 0-based position separated by a ':'.

The 2nd field is the record type, <code>POS</code>, <code>EMPTY</code>, <code>REF_ONLY</code>, or <code>DETAILED</code>.

<code>POS</code> and <code>EMPTY</code> records have no additional columns.

<code>REF_ONLY</code> records have 3 additional fields:
# numBases - the number of bases at this position
# GLH - the GLH for this position
# 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==

BamUtil: asp - Revision history

Mktrost at 21:38, 3 January 2014

Mktrost at 19:40, 21 March 2012

Mktrost: Update rules used for creating the ASP

Mktrost at 21:08, 27 January 2012

Mktrost: Created page with 'asp Category:BAM Software Category:Software = Overview of the asp function of bamUtil = The asp option on the…'

Mktrost: Created page with 'asp Category:BAM Software Category:Software = Overview of the `asp` function of `bamUtil` = The `asp` option on the…'