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===Variant filtration pipeline=== * To run the pipeline, issue the following terminal command from the folder you uploaded the .info file to (in this case /home/ajgore/TestRun): nohup /home/ajgore/AG_Ext12T/GATK_01022012/variantFiltration-latest/variantFiltration.pl prefix.snp.raw.vcf prefix.fixed.bam genome-miner &> prefix.filter.status & * The first argument should be the .vcf file, the second argument should be the .fixed.bam file, and the third argument should be the system (either genome-miner or triton) * You can monitor the status of the pipeline by looking at the "prefix.status" file using less: less prefix.filter.status * The output of the pipeline will be five files: ** prefix.ind.filtered.vcf - VCF file containing filtered indel calls both passing and failing filters (GATK Best Practices Exome v3 Filters) ** prefix.snp.filtered.GATK_New.vcf - VCF file containing snp calls both passing and failing filters (GATK Best Practices Exome v3 Filters) ** prefix.snp.GATK_New.pileup - Pileup file containing filtered snp calls ONLY (GATK Best Practices Exome v3 Filters) ** prefix.snp.filtered.GATK_Old.vcf - VCF file containing snp calls both passing and failing filters (GATK Best Practices Exome v1 Filters) ** prefix.snp.GATK_Old.pileup - Pileup file containing filtered snp calls ONLY (GATK Best Practices Exome v1 Filters)
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