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= Overview of the <code>trimBam</code> function of <code>bamUtil</code> =
= Overview of the <code>trimBam</code> function of <code>bamUtil</code> =
The <code>trimBam</code> option on the [[bamUtil]] executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
The <code>trimBam</code> option on the [[bamUtil]] executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping (if command-line option, <code>--clip</code> is specified).
= Usage =
= Usage =
Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.
Optionally --ignoreStrand/-i can be specified to ignore the strand information and treat forward/reverse the same.
trimBam will modify the sequences to 'N', and the quality string to '!'
trimBam will modify the sequences to 'N', and the quality string to '!' unless the optional parameter --clip/-c is specified. If --clip/-c is specified, the ends will be soft clipped instead of modified.
== Soft Clipping Notes (--clip/-c) ==
Available in version 1.0.14 and later.
When soft clipping:
:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
:* mate information is not updated (start positions/mapping may change after soft clipping)
:** run samtools fixmate to fix mate information (will first need to sort by read name)
:* output is not sorted (start positions/mapping may change after soft clipping)
:** run samtools sort to resort by coordinate (after fixmate)
:* soft clips already in the read are maintained or added to
:** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
:** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
=== Fixing the mate/resorting ===
In order to update the mate, samtools fixmate must be run.
In order to reorder the file, samtools sort must be run.
Notes about the samtools programs:
* samtools fixmate requires the file to be sorted by query name.
* samtools sort cannot write to pipes.
====Steps====
# Run this program and pipe it into samtools sort by query name
#* <pre>./bam trimBam <your InputFile> - [#basesToTrim] [any other options] -c | samtools sort -n - tempQuerySort</pre>
# Run samtools fixmate and pipe it into samtools sort by position
#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>
= Parameters =
= Parameters =
Optional Parameters:
Optional Parameters:
--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
--ignoreStrand : ignore strand information - do not reverse left/right for reverse reads
--clip : soft clip the ends rather than setting to N/!
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== Required Parameters==
== Required Parameters==
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{{OutBAMOutputFile|noParam=2nd}}
==Optional parameters==
==Optional parameters==
=== Number of Bases to Trim from Each End (3rd argument) ===
=== Number of Bases to Trim from Each End (3rd argument) ===
If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.
If the 3rd argument a number (with no flag/option), it is the number of bases to trim from each end of the reads.
===Trim Bases from the Left (<code>--left</code> or <code>--L</code>)===
===Trim Bases from the Left (<code>--left</code> or <code>-L</code>)===
Use <code>--left</code> or <code>--L</code> followed by the number of bases to be trimmed from the left.
Use <code>--left</code> or <code>-L</code> followed by the number of bases to be trimmed from the left.
By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.
By default reverse strands are reversed and then the left is trimmed, meaning that <code>--left</code> actually trims from the right of the read in the SAM/BAM for reverse reads.
Use [[#Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
Use [[#Ignore the Strand when Trimming (--ignoreStrand or -i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
===Trim Bases from the Right (<code>--right</code> or <code>--R</code>)===
===Trim Bases from the Right (<code>--right</code> or <code>-R</code>)===
Use <code>--right</code> or <code>--R</code> followed by the number of bases to be trimmed from the right.
Use <code>--right</code> or <code>-R</code> followed by the number of bases to be trimmed from the right.
By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.
By default reverse strands are reversed and then the right is trimmed, meaning that <code>--right</code> actually trims from the left of the read in the SAM/BAM for reverse reads.
Use [[#Ignore the Strand when Trimming (--ignoreStrand or --i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
Use [[#Ignore the Strand when Trimming (--ignoreStrand or -i)|--ignoreStrand/-i]] to ignore the strand information and treat forward/reverse the same.
=== Ignore the Strand when Trimming (<code>--ignoreStrand</code> or <code>-i</code>) ===
Use <code>--ignoreStrand</code> or <code>-i</code> to ignore the strand information and treat forward/reverse the same. When <code>--ignoreStrand</code> or <code>-i</code> is set, do not reverse reverse reads prior to trimming left/right.
=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===
Use <code>--clip</code> or <code>-c</code> to soft clip the ends instead of setting to N/! (or set to unmapped if the entire read would be soft clipped).
See [[#Soft Clipping Notes (--clip/-c)|Soft Clipping Notes]] for more information about clipping and post processing that will need to be done.
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