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:
-jar GenomeAnalysisTK.jar \
-T ContEst \
-R reference.fasta \
-I:eval tumor.bam \
-I:genotype normal.bam \
--popfile populationAlleleFrequencies.vcf \
[-L targets.interval_list] \
-isr INTERSECTION \
--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".