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

   1 ---
   2 layout: default
   3 navsection: userguide
   4 navmenu: Examples
   5 title: "Crunch examples"
   6
   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 |samtools_tgz|Collection with the samtools source distribution.|@c777e23cf13e5d5906abfdc08d84bfdb+74@|
  22 |input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
  23 </div>
  24
  25 h4. bwa-index
  26
  27 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
  28
  29 <div class="offset1">
  30 table(table table-bordered table-condensed).
  31 |_Parameter_|_Description_|_Example_|
  32 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  33 |input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  34 </div>
  35
  36 h4. picard-gatk2-prep
  37
  38 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
  39
  40 <div class="offset1">
  41 table(table table-bordered table-condensed).
  42 |_Parameter_|_Description_|_Example_|
  43 |input|Collection containing aligned bam files.||
  44 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  45 |reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  46 </div>
  47
  48 h4. GATK2-realign
  49
  50 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
  51
  52 <div class="offset1">
  53 table(table table-bordered table-condensed).
  54 |_Parameter_|_Description_|_Example_|
  55 |input|Collection containing aligned bam files.||
  56 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  57 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  58 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  59 |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)|
  60 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  61 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  62 </div>
  63
  64 h4. GATK2-bqsr
  65
  66 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
  67
  68 <div class="offset1">
  69 table(table table-bordered table-condensed).
  70 |_Parameter_|_Description_|_Example_|
  71 |input|Collection containing bam files.||
  72 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  73 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  74 </div>
  75
  76 h4. GATK2-merge-call
  77
  78 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
  79
  80 <div class="offset1">
  81 table(table table-bordered table-condensed).
  82 |_Parameter_|_Description_|_Example_|
  83 |input|Collection containing bam files.||
  84 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  85 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  86 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  87 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  88 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  89 </div>
  90
  91 h4. file-select
  92
  93 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
  94
  95 <div class="offset1">
  96 table(table table-bordered table-condensed).
  97 |_Parameter_|_Description_|_Example_|
  98 |names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
  99 </div>