From Genome Analysis Wiki
Jump to: navigation, search

BamUtil: trimBam

26 bytes added, 23:28, 12 November 2017
Soft Clipping Notes (--clip/-c)
== Soft Clipping Notes (--clip/-c) ==
(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
# Run samtools fixmate and pipe it into samtools sort by position
#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>
= Parameters =

Navigation menu