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layout: default
navsection: userguide
title: "Scripts provided by Arvados"
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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>