doc/user/examples/crunch-examples.html.textile.liquid

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   2 layout: default
   3 navsection: userguide
   4 title: "Scripts provided by Arvados"
   5 ...
   6
   7 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.
   8
   9 h4. bwa-aln
  10
  11 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
  12
  13 <div class="offset1">
  14 table(table table-bordered table-condensed).
  15 |_Parameter_|_Description_|_Example_|
  16 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  17 |samtools_tgz|Collection with the samtools source distribution.|@c777e23cf13e5d5906abfdc08d84bfdb+74@|
  18 |input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
  19 </div>
  20
  21 h4. bwa-index
  22
  23 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
  24
  25 <div class="offset1">
  26 table(table table-bordered table-condensed).
  27 |_Parameter_|_Description_|_Example_|
  28 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  29 |input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  30 </div>
  31
  32 h4. picard-gatk2-prep
  33
  34 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
  35
  36 <div class="offset1">
  37 table(table table-bordered table-condensed).
  38 |_Parameter_|_Description_|_Example_|
  39 |input|Collection containing aligned bam files.||
  40 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  41 |reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  42 </div>
  43
  44 h4. GATK2-realign
  45
  46 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
  47
  48 <div class="offset1">
  49 table(table table-bordered table-condensed).
  50 |_Parameter_|_Description_|_Example_|
  51 |input|Collection containing aligned bam files.||
  52 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  53 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  54 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  55 |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)|
  56 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  57 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  58 </div>
  59
  60 h4. GATK2-bqsr
  61
  62 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
  63
  64 <div class="offset1">
  65 table(table table-bordered table-condensed).
  66 |_Parameter_|_Description_|_Example_|
  67 |input|Collection containing bam files.||
  68 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  69 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  70 </div>
  71
  72 h4. GATK2-merge-call
  73
  74 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
  75
  76 <div class="offset1">
  77 table(table table-bordered table-condensed).
  78 |_Parameter_|_Description_|_Example_|
  79 |input|Collection containing bam files.||
  80 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  81 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  82 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  83 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  84 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  85 </div>
  86
  87 h4. file-select
  88
  89 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
  90
  91 <div class="offset1">
  92 table(table table-bordered table-condensed).
  93 |_Parameter_|_Description_|_Example_|
  94 |names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
  95 </div>