executing-plans
executing-plans
Use when executing an implementation plan in the current session as the implementer yourself — your human partner chose inline execution, or no subagent tool is available
samtools-bam-processingCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
Independent GitHub snapshot · Automated classification · Original documentation governs