= Allele Counting SOP = This method can be used to create a SNP list across multiple samples and establish the allele count for each variant. == Step 1: Merge samples vcf using GATK !CombineVariants == Merge sample vcf using [http://www.broadinstitute.org/gsa/wiki/index.php/CombineVariants CombineVariants] Semi-code: {{{ cd ~/projects/yourproject/rawdata java -Xmx2g -jar /target/gpfs2/gcc/tools/GATK-1.1-23-g8072bd9/Sting/dist/GenomeAnalysisTK.jar\ -T CombineVariants\ -B:sample1,VCF sample1.all.snp.txt.vcf\ -B:sample2,VCF sample2.all.snp.txt.vcf\ -B:sample3,VCF sample3.all.snp.txt.vcf\ -B:sample4,VCF sample4.all.snp.txt.vcf\ -R /target/gpfs2/gcc/resources/hg19/indices/hg19.fa\ -o union.vcf }}} == Step 2: count alleles using VCF tools == Count allele using [http://vcftools.sourceforge.net/options.html#stats VCFtools]. Semicode: {{{ }}} TODO TODO