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Skills tagged: bcftools

Browse skills that share this tag.

  • bio-consensus-sequences - Generate consensus FASTA sequences from VCF variants
    bioinformaticsbcftoolsvcffasta

    ★ 18 · Updated 2026-09-24

    Generates consensus FASTA sequences by applying VCF variants to a reference sequence using bcftools consensus.

    ⚙ Apply VCF variants to reference⚙ Extract sample specific haplotypes⚙ Encode IUPAC ambiguity codes
  • pysam - Python module for reading and writing genomic datasets
    bioinformaticsgenomicsngspysam

    ★ 0 · Updated 2026-09-21

    Reads, writes, and manipulates SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ genomic sequences using a Pythonic interface to htslib.

    ⚙ Read and write alignment files⚙ Perform pileup coverage analysis⚙ Read and write variant files
  • bio-variant-calling - Variant Calling with bcftools from BAM Alignments
    variant callingbcftoolsSNP detectionindel detection

    ★ 190 · Updated 2026-06-30

    Detect SNPs and indels from aligned reads using bcftools mpileup and call pipeline, generating VCF output from BAM files.

    ⚙ Call SNPs and indels from BAM⚙ Generate pileup from aligned reads⚙ Call variants for specific regions