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-layout: default
-navsection: userguide
-title: "Scripts provided by Arvados"
-...
-
-Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://arvados.org/projects/arvados/repository/revisions/master/show/crunch_scripts. 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. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-aln
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
-|samtools_tgz|Collection with the samtools source distribution.|@c777e23cf13e5d5906abfdc08d84bfdb+74@|
-|input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
-</div>
-
-h4. bwa-index
-
-Generate an index of a fasta reference genome suitable for use by bwa-aln. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-index
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
-|input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
-</div>
-
-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. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/picard-gatk2-prep
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|input|Collection containing aligned bam files.||
-|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
-|reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
-</div>
-
-h4. GATK2-realign
-
-Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-realign
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|input|Collection containing aligned bam files.||
-|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
-|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
-|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
-|known_sites|List of files in the data bundle to use as GATK @-known@ arguments. Optional. |@["dbsnp_137.b37.vcf","Mills_and_1000G_gold_standard.indels.b37.vcf"]@ (this is the default value)|
-|regions|Collection with .bed files indicating sequencing target regions. Optional.||
-|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
-</div>
-
-h4. GATK2-bqsr
-
-Run GATK's BaseQualityScoreRecalibration module on a set of BAM files. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-bqsr
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|input|Collection containing bam files.||
-|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
-|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
-</div>
-
-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. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-merge-call
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|input|Collection containing bam files.||
-|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
-|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
-|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
-|regions|Collection with .bed files indicating sequencing target regions. Optional.||
-|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
-</div>
-
-h4. file-select
-
-Pass through the named files from input to output collection, and ignore the rest. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/file-select
-
-<div class="offset1">
-table(table table-bordered table-condensed).
-|_Parameter_|_Description_|_Example_|
-|names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
-</div>