sniffles(1) on Linux
The text 962447379589, as Debian 12 (Bookworm) shipped it.
structural variation caller using third-generation sequencing
Flags it lists
-
--cluster-binsize -
--cluster-merge-bnd -
--cluster-merge-len -
--cluster-merge-pos -
--cluster-r -
--cluster-repeat-h -
--cluster-repeat-h-max -
--combine-consensus -
--combine-high-confidence -
--combine-low-confidence -
--combine-low-confidence-abs -
--combine-match -
--combine-null-min-coverage -
--combine-output-filtered -
--combine-separate-intra -
--detect-large-ins -
--genotype-error -
--genotype-ploidy -
--genotype-vcf -
--help -
--long-del-coverage -
--long-del-length -
--long-dup-coverage -
--long-dup-length -
--long-ins-length -
--mapq -
--max-del-seq-len -
--max-splits-base -
--max-splits-kb -
--min-alignment-length -
--minsupport -
--minsupport-auto-mult -
--minsvlen -
--minsvlen-screen-ratio -
--no-consensus -
--no-progress -
--no-qc -
--no-sort -
--non-germline -
--output-rnames -
--phase -
--phase-conflict-threshold -
--qc-coverage -
--qc-stdev -
--qc-stdev-abs-max -
--qc-strand -
--quiet -
--reference -
--sample-id -
--snf -
--symbolic -
--tandem-repeats -
--threads -
--vcf -
--version -
-h -
-t -
-v