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==Instructions== ===Gather necessary files=== * Two output files from mapping pipeline are required: ** '''.fixed.bam''' file ** '''.snp.raw.vcf''' file * Either run the pipeline in the same directory as these files or use the full paths to these files in the command below. ===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) ===variant candidate filtering=== *location of scripts on genome-miner: /home/zhl002/bin/getPileupFromVCF.pl $progenitor(/contol).fixed.bam $sample.snp.filtered.fixed.vcf > $control.$sample.pileup /home/zhl002/bin/getPileupFromVCF.pl $sample.fixed.bam $sample.snp.filtered.fixed.vcf > $sample.$sample.pileup /home/zhl002/bin/pileup2variantsPair.pl $control.$sample.pileup $sample.$sample.pileup > $sample.snc grep GOH $sample.snc | grep -v rs | grep "=0" > $sample.snc.filtered *first two lines make a limited pileup file for both the comtrol and the sample * then you do the subtraction and apply the filter * filters listed above as example: # only look at gains of heterozygosity (grep GOH), # only look at non-dbsnp sites (grep -v rs) # only consider cases where we don't see the minor allele in the control # the other filters (chi-sq test, etc) are done inside the perl script, but leave these three outside so we can look at the unfiltered .snc file and the filtered
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