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URL: https://bitbucket.org/dries_decap/halvadeforspark/
Proper Citation: Halvade Somatic (RRID:SCR_021771)
Description: Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run.
Synonyms: Halvade for Spark
Resource Type: software resource
Keywords: somatic variant, GATK, Halvade, VCF output file, germline, somatic variant calling, Spark framework
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