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title: "Crunch examples"
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h1. Crunch examples

Several crunch scripts are included with Arvados in the @/crunch_scripts@ directory. They are intended to provide examples and starting points for writing your own scripts.

h4. bwa-aln

Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair.

h4. bwa-index

Generate an index of a fasta reference genome suitable for use by bwa-aln.

h4. picard-gatk2-prep

Using the FixMateInformation, SortSam, ReorderSam, AddOrReplaceReadGroups, and BuildBamIndex modules from picard, prepare a BAM file for use with the GATK2 tools. Additionally, run picard's CollectAlignmentSummaryMetrics module to produce a @*.casm.tsv@ statistics file for each BAM file.

h4. GATK2-bqsr

Run GATK's BaseQualityScoreRecalibration module on a set of BAM files.

h4. GATK2-merge-call

Merge a set of BAM files using picard, and run GATK's UnifiedGenotyper module on the merged set to produce a VCF file.

h4. GATK2-realign

Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files.

