Package org.broadinstitute.hellbender.tools.spark.pipelines
package org.broadinstitute.hellbender.tools.spark.pipelines
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ClassesClassDescriptionThe full BQSR pipeline in one tool to run on Spark.Runs BWA and MarkDuplicates on Spark.Calculate the overall number of bases SAM/BAM/CRAM fileCalculate the overall number of reads in a SAM/BAM fileSpark tool to accumulate flag statistics given a BAM file, e.g.Print out variants from a VCF file.ReadsPipelineSpark is our standard pipeline that takes unaligned or aligned reads and runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller.SortSam on Spark (works on SAM/BAM/CRAM)