ContEst output

I'm using ContEst for quantification of sample contamination and the commandline used is as follows:
java -Xmx2400m -jar /contest-1.0.24530-bin/ContEst.jar \
-T Contamination \
-I Sample1.bam \
-R hg19.fa \
-B:pop,vcf hg19_hapmap.vcf \
-B:genotypes,vcf Sample1.vcf \
-BTI genotypes \
-L Target.bed \
-o Sample1.out.txt

It generated an output:
_name population population_fit contamination confidence_interval_95_width confidence_interval_95_low confidence_interval_95_high sites
META CEU n/a 0.1 0.1 0.1 0.2 1742

and the contamination is 0.1% (and also for other samples as well), which seems unrealistic, as I'm expecting around 10%,
whats happening?

Thank you!


  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    You're expecting 10% cross-patient contamination in your dataset? Just want to be sure that you're not expecting ContEst to estimate the purity of a tumor sample (ie the effect of stromal contamination) as that is not what the method does. It estimates the level of cross-patient contamination. Typically we see <0.5% levels of cross-patient contamination in our production sequencing center (and others as well)

  • achalneupaneachalneupane Member

    I want to ask you why I am getting the output with header line only. It also generates the following error after completing the run
    WARN 13:46:52,103 RestStorageService - Error Response: PUT '/GATK_Run_Reports/' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1322, Content-MD5: OnDX6l+TYlPWxt+iqbSLwQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 3a70d7ea5f936253d6c6dfa2a9b48bc1, Date: Fri, 03 Jun 2016 03:46:50 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:5iT6W7TwgPmleMi0YLXeLzjdq6s=, User-Agent: JetS3t/0.8.0 (Linux/2.6.32-573.26.1.el6.x86_64; amd64; en; JVM 1.6.0_30), Host:, Expect: 100-continue], Response Headers: [x-amz-request-id: C481571B466F9733, x-amz-id-2: aaSqXmyM5i9kUlTnOvD19HLqh6duRFFyprSgXlQ7cJfhb0H8OJYPbbc3Q3KJuFWwnVqyRuHftck=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Fri, 03 Jun 2016 03:46:51 GMT, Connection: close, Server: AmazonS3]

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    It looks like an issue with the Phone Home system. Usually the warning does not affect the output, however. Have a look at this thread. Can you tell us the exact command you are running? Also, it looks like you are using Java 1.6. GATK (latest version 3.6) only runs with Java 1.8.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi again,

    I should also point out that with the latest version, there is no more Phone Home! :smile:


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