samclip
filter SAM file for soft and hard clipped alignments
Command lineScience
Not tested on a device yet. What that means
Commands in the package
samclip
About samclip
From Debian's package description
Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in --end-to-end mode). This means the ends of the read may not be part of the best alignment.
This can be caused by:
- adapter sequences (aren't in the reference)
- poor quality bases (mismatches only make the alignment score worse)
- structural variation in your sample compared to the reference
- reads overlapping the start and end of contigs (including circular genomes)
Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which describes which parts of the read aligned and which didn't. The unaligned ends of the read can be "soft" or "hard" clipped, denoted with S and H at each end of the CIGAR string. It is possible for both types to be present, but that is not common. Soft and hard don't mean anything biologically, they just refer to whether the full read sequence is in the SAM file or not.
From Debian's description of the samclip package, under that package's license.
Dependencies
Depends on
Related apps
- picard-toolsCommand line tools to manipulate SAM and BAM filesCommand line
- staden-io-lib-utilsprograms for manipulating DNA sequencing filesCommand line
- bamtoolstoolkit for manipulating BAM (genome alignment) filesCommand line
- pbbamtoolsprocessing Pacific Biosciences binary alignment/map filesCommand line
- ardenspecificity control for read alignments using an artificial referenceCommand line
- bamclipperRemove gene-specific primer sequences from SAM/BAM alignmentsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the samclip package, under that package's license.
- Description: Debian's description of the samclip package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.