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Use when you need to connect to the SciGraph SCP server for PertKGE (knowledge graph for compound-protein interaction inference using perturbation transcriptomics + regulatory network; cold-start CPI prediction) and call its MCP tools (query_cypher, get_kg_statistics, get_entity_details, get_expe...
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller or when highest germline calling accuracy is required.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
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