text: user1771: 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
  
  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".
  
  user77: On the GATK forum they've recommended the population stratified VCF file for this purpose.
  
original_text: 1771: <p>I want to use <a href="https://software.broadinstitute.org/gatk" rel="nofollow noreferrer">GATK</a> to estimate cross-sample contamination for Whole Genome Sequencing data.</p>
  
  <p>The specific tool is <a href="https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_cancer_contamination_ContEst.php" rel="nofollow noreferrer">ContEst</a> and it is run with:</p>
  
  <pre><code>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
  </code></pre>
  
  <p>The <code>--popfile</code> option requires a vcf file representing population allele frequencies. Where can I get it? Is it the one I can get from <a href="https://www.ncbi.nlm.nih.gov/projects/SNP/index.html" rel="nofollow noreferrer">dbSNP</a>?</p>
  
  <p>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".</p>
   77: <p>On the <a href="https://gatkforums.broadinstitute.org/gatk/discussion/8897/which-one-should-i-use-for-contest-popfile" rel="noreferrer">GATK forum</a> they've recommended <a href="ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3_b37_pop_stratified_af.vcf.gz" rel="noreferrer">the population stratified VCF file</a> for this purpose.</p>
  