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 ​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 ​VCFtools. Semicode:

TODO