octopus-variant-calling
End-to-end variant calling pipeline from paired-end FASTQ reads using Octopus, a haplotype-aware Bayesian variant caller. Includes quality control (FastQC), adapter trimming (fastp), read alignment (BWA-MEM2), haplotype-based variant detection (Octopus), and quality filtering (bcftools). Detects SNPs, indels, and complex variants using particle filtering.
VERSION 1.0.0
AUTHOR khyeonm
INPUT Paired-end FASTQ (R1, R2)Reference genome FASTA
OUTPUT Filtered VCFVariant statistics TXTFastQC HTML reportfastp HTML report
FILES
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