Analyze BAM/SAM/CRAM files for reads, indels, and coverage with JSON output.
npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill bam-toolkit
Please help me install this Agent Skill. Skill: bam-toolkit Source: https://github.com/dakesan/cc-dnawork-plugin/tree/main/scientific-skills/bam-toolkit Command: npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill bam-toolkit
This Skill helps you analyze BAM/SAM/CRAM alignment files from WGS/WES, including region-based read extraction, indel detection, and coverage statistics, with structured JSON outputs for downstream analysis.
Extract reads in chr1:1000-2000 as JSON, or compute coverage for the same region.
High-intent search queries and answers about installing and using this skill.
Extract reads from BAM files by specifying a genomic region (e.g., chr1:1000-2000) and applying CLI filters like min_mapq and min_baseq. The Skill outputs matched reads in JSON or BAM format for downstream analysis.
Indel detection identifies insertions and deletions from reads in BAM/SAM/CRAM files. The Skill parses alignment records and outputs structured JSON containing indel positions, lengths, and read context for variant workflows.
Compute per-region coverage statistics by submitting BAM alignment files and target regions. The Skill calculates coverage metrics and exports results as JSON, enabling integration into region-based analysis pipelines.
Coverage analysis, read extraction, and indel detection work across BAM, SAM, and CRAM formats. The Skill uses pysam to handle all three alignment formats transparently with consistent JSON output.
Filter reads during extraction using min_mapq and min_baseq parameters, plus options for proper-pairs and duplicate removal. These CLI filters refine results before JSON/BAM export for high-confidence downstream use.
Region-based processing scales to large WGS datasets by processing defined intervals independently. Performance depends on region size and BAM indexing; very large regions or unindexed files may require longer computation.
qinyan-aiProcess SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files via Python.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
shushuznParse and analyze NGS alignment, variant, and sequence files with pysam.
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