Tools for working with genomic and high throughput sequencing data.

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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

Paired end reads that map to a given amplicon position are trimmed so that the alignment no-longer includes the primer sequences. All other aligned reads have the maximum primer length trimmed!

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.


Name Flag Type Description Required? Max 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