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 populationSites.interval_list
 [-L targets.interval_list] \
 -o output.txt

The --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".


1 Answer 1


On the GATK forum they've recommended the population stratified VCF file for this purpose.


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