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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.
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.
* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
== Soft Clipping Notes (--clip/-c) ==
* mate information is not updated (start positions/mapping may change after soft clipping)
When soft clipping:
** run samtools fixmate to fix mate information (will first need to sort by read name)
:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
* output is not sorted (start positions/mapping may change after soft clipping)
:* mate information is not updated (start positions/mapping may change after soft clipping)
** run samtools sort to resort by coordinate (after fixmate)
:** run samtools fixmate to fix mate information (will first need to sort by read name)
* soft clips already in the read are maintained or added to
:* output is not sorted (start positions/mapping may change after soft clipping)
** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
:** run samtools sort to resort by coordinate (after fixmate)
** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
:* 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 =
=== SoftClip the Ends (<code>--clip</code> or <code>-c</code>) ===
=== 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/!.
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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