doc/user/crunch-examples.textile

   1 ---
   2 layout: default
   3 navsection: userguide
   4 title: "Crunch examples"
   5 navorder: 30
   6 ---
   7
   8 h1. Crunch examples
   9
  10 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.
  11
  12 h4. bwa-aln
  13
  14 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
  15
  16 <div class="offset1">
  17 table(table table-bordered table-condensed).
  18 |_Parameter_|_Description_|_Example_|
  19 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  20 |input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
  21 </div>
  22
  23 h4. bwa-index
  24
  25 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
  26
  27 <div class="offset1">
  28 table(table table-bordered table-condensed).
  29 |_Parameter_|_Description_|_Example_|
  30 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  31 |input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  32 </div>
  33
  34 h4. picard-gatk2-prep
  35
  36 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
  37
  38 <div class="offset1">
  39 table(table table-bordered table-condensed).
  40 |_Parameter_|_Description_|_Example_|
  41 |input|Collection containing aligned bam files.||
  42 |picard_zip|Collection with the picard binary distribution.||
  43 |reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  44 </div>
  45
  46 h4. GATK2-realign
  47
  48 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
  49
  50 <div class="offset1">
  51 table(table table-bordered table-condensed).
  52 |_Parameter_|_Description_|_Example_|
  53 |input|Collection containing aligned bam files.||
  54 |picard_zip|Collection with the picard binary distribution.||
  55 |gatk_tbz|Collection with the GATK2 binary distribution.||
  56 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  57 |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)|
  58 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  59 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  60 </div>
  61
  62 h4. GATK2-bqsr
  63
  64 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
  65
  66 <div class="offset1">
  67 table(table table-bordered table-condensed).
  68 |_Parameter_|_Description_|_Example_|
  69 |input|Collection containing bam files.||
  70 |gatk_tbz|Collection with the GATK2 binary distribution.||
  71 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  72 </div>
  73
  74 h4. GATK2-merge-call
  75
  76 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
  77
  78 <div class="offset1">
  79 table(table table-bordered table-condensed).
  80 |_Parameter_|_Description_|_Example_|
  81 |input|Collection containing bam files.||
  82 |picard_zip|Collection with the picard binary distribution.||
  83 |gatk_tbz|Collection with the GATK2 binary distribution.||
  84 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  85 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  86 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  87 </div>
  88
  89 h4. file-select
  90
  91 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
  92
  93 <div class="offset1">
  94 table(table table-bordered table-condensed).
  95 |_Parameter_|_Description_|_Example_|
  96 |names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
  97 </div>