navsection: userguide
title: "Scripts provided by Arvados"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
-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.
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+{% include 'pipeline_deprecation_notice' %}
+
+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.
h4. bwa-aln
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).
h4. bwa-index
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).
h4. picard-gatk2-prep
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).
h4. GATK2-realign
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).
h4. GATK2-bqsr
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).
h4. GATK2-merge-call
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).
h4. file-select
-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
+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
<div class="offset1">
table(table table-bordered table-condensed).