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Revision as of 17:49, 22 December 2011
, 17:49, 22 December 2011Created page with 'clipOverlap Category:BAM Software Category:Software = Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> = The <code>ind…'
[[Category:BamUtil|clipOverlap]]
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =
The <code>indelDiscordance</code> option on the [[bamUtil]] looks at discordance at sites on the male X chromosome.
== ASSUMPTIONS/RESTRICTIONS ==
= Usage =
./bam indelDiscordance --in <inputFile> [--bamIndex <bamIndexFile] [--refFile <filename>] [--umRef] [--depth minDepth] [--minRepeatLen len] [--sumRepeatLen len] [--printPos] [--chrom <name>] [--start 0basedPos] [--end 0basedPos] [--noeof] [--params]
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to calculate indelDiscordance for
Optional Parameters:
--bamIndex : The path/name of the bam index file
(if required and not specified, uses the --in value + ".bai")
--refFile : reference file for determining repeat counts
--umRef : use the reference at the default UofM location, /data/local/ref/karma.ref/human.g1k.v37.umfa
--depth : min depth at which to report indel discordance, DEFAULT >= 3
--minRepeatLen : min repeat length for printing repeat info, DEFAULT = 1
--sumRepeatLen : all repeats this length and longer will be accumulated,
DEFAULT = 5
--printPos : print details for each position
--chrom : chromosome name other than X
--start : use a 0-based inclusive start position other than the default, 2699520
--end : use a 0-based exclusive end position other than the default, 154931043
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings
</pre>
{{inBAMInputFile}}
{{bamIndex}}
{{refFile}}
{{noeofBGZFParameter}}
{{paramsParameter}}
= Return Value =
= Output =
All status messages are written to stderr.
== Example Output ==
<pre>
</pre>
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =
The <code>indelDiscordance</code> option on the [[bamUtil]] looks at discordance at sites on the male X chromosome.
== ASSUMPTIONS/RESTRICTIONS ==
= Usage =
./bam indelDiscordance --in <inputFile> [--bamIndex <bamIndexFile] [--refFile <filename>] [--umRef] [--depth minDepth] [--minRepeatLen len] [--sumRepeatLen len] [--printPos] [--chrom <name>] [--start 0basedPos] [--end 0basedPos] [--noeof] [--params]
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to calculate indelDiscordance for
Optional Parameters:
--bamIndex : The path/name of the bam index file
(if required and not specified, uses the --in value + ".bai")
--refFile : reference file for determining repeat counts
--umRef : use the reference at the default UofM location, /data/local/ref/karma.ref/human.g1k.v37.umfa
--depth : min depth at which to report indel discordance, DEFAULT >= 3
--minRepeatLen : min repeat length for printing repeat info, DEFAULT = 1
--sumRepeatLen : all repeats this length and longer will be accumulated,
DEFAULT = 5
--printPos : print details for each position
--chrom : chromosome name other than X
--start : use a 0-based inclusive start position other than the default, 2699520
--end : use a 0-based exclusive end position other than the default, 154931043
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings
</pre>
{{inBAMInputFile}}
{{bamIndex}}
{{refFile}}
{{noeofBGZFParameter}}
{{paramsParameter}}
= Return Value =
= Output =
All status messages are written to stderr.
== Example Output ==
<pre>
</pre>
