<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>

CC BY-SA 3.0
2017-12-13T20:52:44.337Z
2017-12-13T20:52:44.337Z
Devon Ryan
<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>

<vcf><variant-calling><gatk><quality-control><wgs>
Where can I get the population allele frequency vcf file?
# Where can I get the population allele frequency vcf file?

(Asked by: username_0 on 2017-12-13)

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".

**Tags:** vcf, variant-calling, gatk, quality-control, wgs

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## 1 answers

### Answer by username_1 on 2017-12-13. Score: 5 | Accepted answer

On the [GATK forum](https://gatkforums.broadinstitute.org/gatk/discussion/8897/which-one-should-i-use-for-contest-popfile) they've recommended [the population stratified VCF file](ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3_b37_pop_stratified_af.vcf.gz) for this purpose.


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