doc/user/examples/crunch-examples.textile

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