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Revision as of 11:59, 11 June 2014
, 11:59, 11 June 2014no edit summary
Look at FASTQ:
Look at FASTQ:
less -S ${GC}/inputs/fastq/HG00641.chr7.CFTR.SRR069531.fastq
less -S ${GC}/inputs/fastq/HG00641.chr7.CFTR.SRR069531_1.fastq
<code>less</code> is a Linux command that allows you to look at a file.
<code>less</code> is a Linux command that allows you to look at a file.
*<code>-S</code> option prevents line wrap.
*<code>-S</code> option prevents line wrap.
** 1000G_omni2.5.b37.sites.PASS.chr7.vcf.gz.tbi
** 1000G_omni2.5.b37.sites.PASS.chr7.vcf.gz.tbi
** Used for variant filtering
** Used for variant filtering
* INDEL sites
** 1kg.pilot_release.merged.indels.sites.hg19.chr7.vcf
** Used for variant calling
==== GotCloud FASTQ Index File ====
==== GotCloud FASTQ Index File ====
Sample2 fastq/S2/F2.fastq.gz . RGID2 SampleID2 Lib2 UM ILLUMINA
Sample2 fastq/S2/F2.fastq.gz . RGID2 SampleID2 Lib2 UM ILLUMINA
The <code>--fastq</code>/<code>FASTQ</code> setting can be used to specify a prefix to the FASTQ1/FASTQ2 file paths that should be applied before using the files.
The command-line <code>--fastq</code> option or the configuration file <code>FASTQ_PREFIX</code> setting can be used to specify a prefix to the FASTQ1/FASTQ2 file paths.
This file is specified either via the command-line <code>--index_file</code> parameter or via the configuration file <code>INDEX_FILE</code> setting.
This file is specified either via the command line parameter <code>--index_file</code> or via the configuration file setting <code>INDEX_FILE</code>.
The command-line setting takes precedence over the configuration file setting.
The command-line setting takes precedence over the configuration file setting.
==== GotCloud Configuration File ====
==== GotCloud Configuration File ====
This file is created by you to configure GotCloud for your data.
This file is created by you to configure GotCloud for your data.
* Default values are provided in ${GC}/gotcloud/bin/gotcloudDefaults.conf
** Most values should be left as the defaults
* Specify values in your configuration file as:
KEY = value
* Keys to override:
{|class="wikitable" cellpadding=5
|-
! Key Name !! Description
|-
| colspan=2 style="text-align:center"| Index File Settings - pointing GotCloud to your data
|-
| INDEX_FILE || Path to the FASTQ index file that you created
* Alternatively, this can be specified on the command-line as <code>--index_file</code>
|-
| FASTQ_PREFIX || Prefix to be added to the FASTQ files in INDEX_FILE
* Not required
|-
| BAM_INDEX || Path to the BAM index file
* to be created by alignment
* to be used for snp calling
|-
| colspan=2 style="text-align:center"| Reference File Settings - telling GotCloud where to find your reference files
|-
| REF_DIR || Path to your reference files
* You don't have to use this, you can specify the full path for each file
|-
| REF || Path/filename of the FASTA reference file
* If different than default: $(REF_DIR)/human.g1k.v37.fa
|-
| DBSNP_VCF || Path/filename of the DBSNP file
* If different than default: $(REF_DIR)/dbsnp_135.b37.vcf.gz
|-
| HM3_VCF || Path/filename of the HapMap3 file
* If different than default: $(REF_DIR)/hapmap_3.3.b37.sites.vcf.gz
|-
| OMNI_VCF || Path/filename of the OMNI file
* If different than default: $(REF_DIR)/1000G_omni2.5.b37.sites.PASS.vcf.gz
|-
| INDEL_PREFIX || Path/filename base of the indels file
* If different than default: $(REF_DIR)/1kg.pilot_release.merged.indels.sites.hg19
|}
