I want to use GATK to estimate cross-sample contamination for Whole Genome Sequencing data.
The specific tool is ContEst and it is run with:
java -jar GenomeAnalysisTK.jar \ -T ContEst \ -R reference.fasta \ -I:eval tumor.bam \ -I:genotype normal.bam \ --popfile populationAlleleFrequencies.vcf \ -L populationSites.interval_list [-L targets.interval_list] \ -isr INTERSECTION \ -o output.txt
--popfile option requires a vcf file representing population allele frequencies. Where can I get it? Is it the one I can get from dbSNP?
I'm using the human_g1k_v37.fasta reference, a version of hg19, "for the phase1 analysis we mapped to GRCh37. Our fasta file which can be found here called human_g1k_v37.fasta.gz, it contains the autosomes, X, Y and MT but no haplotype sequence or EBV".