Athurva Gore:LabNotes/ExomePipeline: Difference between revisions

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* First, generate a text file containing your data information.  This file should look like the following:
* First, generate a text file containing your data information.  This file should look like the following:
  mpleID LibraryID FlowCell Lane Barcode File1 File2
  mpleID LibraryID FlowCell Lane Barcode File1 File2
  CV-F AL-Exome-CV-F-PP HL026 s2 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091127_HL026/s_2_sequence.txt.gz
  CV-iF AL-Exome-CV-iF-PP HL022 s5 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_5_sequence.txt.gz
  CV-F AL-Exome-CV-F-PP HL026 s3 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091127_HL026/s_3_sequence.txt.gz
  CV-iF AL-Exome-CV-iF-PP HL022 s6 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_6_sequence.txt.gz
  CV-F AL-Exome-CV-F-PP HL026 s4 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091127_HL026/s_4_sequence.txt.gz
  CV-iF AL-Exome-CV-iF-PP HL022 s7 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_7_sequence.txt.gz
  CV-F AL-Exome-CV-F HL047 s7 NA /media/SeqStore2/100326_HL047/s_7_sequence.txt.gz
  CV-iF AL-Exome-CV-iF-PP HL025 s7 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091123_HL025/s_7_sequence.txt.gz
  CV-F AL-Exome-CV-F HL047 s8 NA /media/SeqStore2/100326_HL047/s_8_sequence.txt.gz
  CV-iF AL-Exome-CV-iF-PP HL026 s5 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091127_HL026/s_5_sequence.txt.gz
CV-iF AL-Exome-CV-iF HL053 s2 NA /media/SeqStore2/100503_HL053/s_2_1_sequence.txt.gz /media/SeqStore2/100503_HL053/s_2_2_sequence.txt.gz
 
===Run pipeline===
===Run pipeline===
* To run the pipeline, issue the following terminal command:
* To run the pipeline, issue the following terminal command:

Revision as of 18:14, 16 February 2012

Human Genome Resequencing Pipeline

  • Pipeline can be found in genome-miner:/home/ajgore/AG_Ext12T/GATK_01022012/variantCallerBwaGATK-latest/variantCallerBwaGATK.pl
    • This link will always point to the updated version
  • Updated on 02/16/2012

Requirements

  • All required files are currently on genome-miner and triton cluster. Below paths list genome-miner locations
  • NCBI Human Genome Reference Sequence, v37 (/home/ajgore/AG_Ext12T/GATK_01022012/resources_1.2/human_g1k_v37.fasta)
  • CCDS BED file (/home/ajgore/AG_Ext12T/GATK_01022012/resources_1.2/CCDS.20120105.UCSC.nochr.bed)
  • dbSNP in VCF format (/home/ajgore/AG_Ext12T/GATK_01022012/resources_1.2/dbsnp_132.b37.vcf)
  • GATK from 01022012 (/home/ajgore/AG_Ext12T/GATK_01022012/GenomeAnalysisTK-1.4-1-g1b6d528/)
  • BWA 0.5.8 or later (/home/kunzhang/softwares/bwa-latest)
  • Samtools 0.1.7 or later (/home/kunzhang/softwares/samtools-latest)
  • Picard-tools 1.38 or later (/home/kunzhang/softwares/picard-tools-latest)

Instructions

Generate data annotation file (.info file)

  • First, generate a text file containing your data information. This file should look like the following:
mpleID	LibraryID	FlowCell	Lane	Barcode	File1	File2
CV-iF	AL-Exome-CV-iF-PP	HL022	s5	NA	/media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_5_sequence.txt.gz	
CV-iF	AL-Exome-CV-iF-PP	HL022	s6	NA	/media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_6_sequence.txt.gz	
CV-iF	AL-Exome-CV-iF-PP	HL022	s7	NA	/media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_7_sequence.txt.gz	
CV-iF	AL-Exome-CV-iF-PP	HL025	s7	NA	/media/Syn_15T/Ext9T_Backup/SeqStore2009/091123_HL025/s_7_sequence.txt.gz	
CV-iF	AL-Exome-CV-iF-PP	HL026	s5	NA	/media/Syn_15T/Ext9T_Backup/SeqStore2009/091127_HL026/s_5_sequence.txt.gz	
CV-iF	AL-Exome-CV-iF	HL053	s2	NA	/media/SeqStore2/100503_HL053/s_2_1_sequence.txt.gz	/media/SeqStore2/100503_HL053/s_2_2_sequence.txt.gz

Run pipeline

  • To run the pipeline, issue the following terminal command:
nohup /home/ajgore/AG_Ext12T/GATK_01022012/variantCallerBwaGATK-latest/variantCallerBwaGATK.pl prefix.info &> prefix.status
  • You can monitor the status of the pipeline by looking at the "prefix.status" file using less:
less prefix.status
  • The output of the pipeline will be two files:
    • {prefix}.fixed.bam
    • {prefix}.snp.raw.vcf

Exome Mutation Calling Pipeline

  • Still working on newest version
  • Testing out VQSR and VarScan as new variant callers