TrimPrimers

Overview

Group: SAM/BAM

Trims primers from reads post-alignment. Takes in a BAM file of aligned reads and a tab-delimited file with five columns (chrom, left_start, left_end, right_start, and right_end) which provide the 1-based inclusive start and end positions of the primers for each amplicon. The primer file must include headers, e.g:

chrom  left_start  left_end  right_start right_end
chr1   1010873     1010894   1011118     1011137

Both paired end reads and fragment reads that map to a given amplicon position are trimmed so that the alignment no-longer includes the primer sequences. This includes both the 5’ and 3’ ends of each read. All other aligned reads have the maximum primer length trimmed from the 5’ end only!

Reads that are trimmed will have the NM, UQ and MD tags cleared as they are no longer guaranteed to be accurate. If a reference is provided the reads will be re-sorted by coordinate after trimming and the NM, UQ and MD tags recalculated.

If the input BAM is not queryname sorted it will be sorted internally so that mate information between paired-end reads can be corrected before writing the output file.

The --first-of-pair option will cause only the first of pair (R1) reads to be trimmed based solely on the primer location of R1. This is useful when there is a target specific primer on the 5’ end of R1 but no primer sequenced on R2 (eg. single gene-specific primer target enrichment), as well as fragment reads. In this case, the location of each target specific primer should be specified in an amplicons left or right primer exclusively. The coordinates of the non-specific-target primer should be -1 for both start and end, e.g:

chrom  left_start  left_end  right_start right_end
chr1   1010873     1010894   -1          -1
chr2   -1          -1        1011118     1011137

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToBam	Input BAM file.	Required	1
output	o	PathToBam	Output BAM file.	Required	1
primers	p	FilePath	File with primer locations.	Required	1
hard-clip	H	Boolean	If true, hard clip reads, else soft clip.	Optional	1	false
slop	S	Int	Match to primer locations +/- this many bases.	Optional	1	5
sort-order	s	SamOrder	Sort order of output BAM file (defaults to input sort order).	Optional	1
ref	r	PathToFasta	Optional reference fasta for recalculating NM, MD and UQ tags.	Optional	1
auto-trim-attributes	a	Boolean	Automatically trim extended attributes that are the same length as bases.	Optional	1	false
first-of-pair		Boolean	Trim only first of pair reads (R1s) or fragment reads, otherwise both ends of a pair.	Optional	1	false