snippy-ng utils aln samclip

Filter clipped reads from a SAM file using a boundary-aware terminal clipping rule.

The command checks the terminal clipping at both ends of each alignment and filters the read when either end exceeds the configured threshold. If a clipped end reaches the contig boundary, that end is ignored. This means reads with large clipped segments can remain when the clipping is explained by the contig edge rather than an internal alignment artifact.

--max-clip-fraction uses the total terminal clipping divided by the original query length, including hard-clipped bases.

Example

Filter clipped alignments with the default maximum terminal clip length:

snippy-ng utils aln samclip --index ref.fa.fai input.sam > clipped.sam

Use only the fraction-based rule:

snippy-ng utils aln samclip \
  --index ref.fa.fai \
  --max-clip-fraction 0.1 \
  input.sam > clipped.sam

Combine the absolute and fraction-based rules:

snippy-ng utils aln samclip \
  --index ref.fa.fai \
  --max 10 \
  --max-clip-fraction 0.1 \
  input.sam > clipped.sam

Options

Option	Purpose
SAM_FILE	Input SAM file. Reads from standard input when omitted.
--index PATH	Reference FASTA index (.fai) for the reference used during alignment.
--fix-mate / --no-fix-mate	Attempt to mark mates as unmapped when one read in a pair is filtered.
--max INT	Maximum terminal clip length to allow on either end, after ignoring clipping at contig boundaries.
--max-clip-fraction FLOAT	Maximum total terminal clipping as a fraction of the original read length, including hard clips.
--invert	Keep only clipped reads instead of filtering them out.
--debug	Write debug information about clipped reads to standard error.

Behavior notes

• --max is applied to each end independently.
• A read is filtered when the left end, the right end, or both exceed the threshold.
• Clipping at the contig boundary is ignored before the comparison.
• --max-clip-fraction measures total terminal clipping, not just soft clips.
• --fix-mate expects queryname-sorted SAM input.