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- | CV-iF AL-Exome-CV-iF-PP HL022 s5 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_5_sequence.txt.gz | ||
CV- | CV-iF AL-Exome-CV-iF-PP HL022 s6 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_6_sequence.txt.gz | ||
CV- | CV-iF AL-Exome-CV-iF-PP HL022 s7 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_7_sequence.txt.gz | ||
CV- | CV-iF AL-Exome-CV-iF-PP HL025 s7 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091123_HL025/s_7_sequence.txt.gz | ||
CV- | 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