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

   1 ---
   2 layout: default
   3 navsection: userguide
   4 title: "Scripts provided by Arvados"
   5 ...
   6 {% comment %}
   7 Copyright (C) The Arvados Authors. All rights reserved.
   8
   9 SPDX-License-Identifier: CC-BY-SA-3.0
  10 {% endcomment %}
  11
  12 {% include 'pipeline_deprecation_notice' %}
  13
  14 Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://dev.arvados.org/projects/arvados/repository/revisions/master/show/crunch_scripts. They are intended to provide examples and starting points for writing your own scripts.
  15
  16 h4. bwa-aln
  17
  18 Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-aln
  19
  20 <div class="offset1">
  21 table(table table-bordered table-condensed).
  22 |_Parameter_|_Description_|_Example_|
  23 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  24 |samtools_tgz|Collection with the samtools source distribution.|@c777e23cf13e5d5906abfdc08d84bfdb+74@|
  25 |input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
  26 </div>
  27
  28 h4. bwa-index
  29
  30 Generate an index of a fasta reference genome suitable for use by bwa-aln. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-index
  31
  32 <div class="offset1">
  33 table(table table-bordered table-condensed).
  34 |_Parameter_|_Description_|_Example_|
  35 |bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
  36 |input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  37 </div>
  38
  39 h4. picard-gatk2-prep
  40
  41 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://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/picard-gatk2-prep
  42
  43 <div class="offset1">
  44 table(table table-bordered table-condensed).
  45 |_Parameter_|_Description_|_Example_|
  46 |input|Collection containing aligned bam files.||
  47 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  48 |reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
  49 </div>
  50
  51 h4. GATK2-realign
  52
  53 Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-realign
  54
  55 <div class="offset1">
  56 table(table table-bordered table-condensed).
  57 |_Parameter_|_Description_|_Example_|
  58 |input|Collection containing aligned bam files.||
  59 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  60 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  61 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  62 |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)|
  63 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  64 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  65 </div>
  66
  67 h4. GATK2-bqsr
  68
  69 Run GATK's BaseQualityScoreRecalibration module on a set of BAM files. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-bqsr
  70
  71 <div class="offset1">
  72 table(table table-bordered table-condensed).
  73 |_Parameter_|_Description_|_Example_|
  74 |input|Collection containing bam files.||
  75 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  76 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  77 </div>
  78
  79 h4. GATK2-merge-call
  80
  81 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://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-merge-call
  82
  83 <div class="offset1">
  84 table(table table-bordered table-condensed).
  85 |_Parameter_|_Description_|_Example_|
  86 |input|Collection containing bam files.||
  87 |picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
  88 |gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
  89 |gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
  90 |regions|Collection with .bed files indicating sequencing target regions. Optional.||
  91 |region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
  92 </div>
  93
  94 h4. file-select
  95
  96 Pass through the named files from input to output collection, and ignore the rest. "View source.":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/file-select
  97
  98 <div class="offset1">
  99 table(table table-bordered table-condensed).
 100 |_Parameter_|_Description_|_Example_|
 101 |names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
 102 </div>