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GATK4,Cann't get right CalculateContamination result

Question regarding CalculateContamination(GATK/4.1.2.0):

With CalculateContamination in tumor matched mode, I get:
contamination error
NaN 1.0

When I look at the tumor.table and normal. table files generated by Getpileupsummaries, I don't see any unusual data structure/value

What can be the problem?

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @yyj

    Can you please post the exact commands you used for Getpileupsummaries and CalculateContamination. Also please post the first few records of the Getpileupsummaries table.

  • yyjyyj Member
    @ bhanuGandham
    The Getpileupsummaries commands as follow:
    for sample in *.bam;
    do
    base=${sample%%.*};
    gatk4 GetPileupSummaries
    -I $sample
    -V ../../reference/somatic-hg38_af-only-gnomad.hg38.SNP_biallelic.vcf.gz
    -O ./contamination/"$base"_getpileupsummaies.table;
    done

    The CalculateContamination commands as follow:
    for sample in *.bam;
    do base=${sample%%.*};
    gatk4 GetPileupSummaries
    -I $sample
    -V ../../reference/somatic-hg38_af-only-gnomad.hg38.SNP_biallelic.vcf.gz
    -L ../../reference/S07604514_hs_hg38/S07604514_hs_hg38/S07604514_Padded.bed
    -O ./contamination/"$base"_getpileupsummaies.table;done
    The first 30 lines of getpileupsummaies.table:
    contig position ref_count alt_count other_alt_count allele_frequency
    chr1 12882 0 0 0 0.021
    chr1 13110 0 0 0 0.149
    chr1 13143 0 0 0 0.05
    chr1 13149 0 0 0 0.011
    chr1 13178 0 0 0 0.061
    chr1 13273 0 0 0 0.115
    chr1 13281 0 0 0 0.04
    chr1 13418 0 0 0 0.183
    chr1 13613 0 0 0 0.02
    chr1 13621 0 0 0 0.011
    chr1 13649 0 0 0 0.054
    chr1 13684 0 0 0 0.027
    chr1 13752 0 0 0 0.018
    chr1 13757 0 0 0 0.021
    chr1 14522 0 0 0 0.05
    chr1 14542 0 0 0 0.072
    chr1 14574 0 0 0 0.101
    chr1 14590 0 0 0 0.097
    chr1 14599 0 0 0 0.123
    chr1 14604 0 0 0 0.125
    chr1 14610 0 0 0 0.128
    chr1 14626 0 0 0 0.011
    chr1 14671 0 0 0 0.011
    chr1 14677 0 0 0 0.058
    chr1 14773 0 0 0 0.016
    chr1 14843 0 0 0 0.018
    chr1 14933 0 0 0 0.158
    chr1 14948 0 0 0 0.055
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited May 2019

    @yyj
    1)
    --intervals is a required argument for GetPileupSummaries, see : https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_contamination_GetPileupSummaries.php

    2)

    The CalculateContamination commands as follow:
    for sample in .bam;
    do base=${sample%%.
    };
    gatk4 GetPileupSummaries

    In this case you are using GetPileupSummaries instead of CalculateContamination. See: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_contamination_CalculateContamination.php

  • RishabhRishabh IndiaMember
    edited July 2019
    I also got the same result as @yyj .The command i use were

    java -jar /PathToGatk4.1.2.0 GetPileupSummaries
    -I tumor.bam
    -V output.vcf
    -L V6.bed
    -O tumor_getpileupsummaries.table

    OUTPUT
    #<METADATA>SAMPLE=Hg19_P1
    contig position ref_count alt_count other_alt_count allele_frequency
    chr1 981727 0 0 0 0.076
    chr1 986538 0 0 0 0.115
    chr1 986541 0 0 0 0.154
    chr1 986545 0 0 0 0.148
    chr1 986549 0 0 0 0.143
    chr1 986557 0 0 0 0.154

    I generated output.vcf by this command (is this approach right)
    COMM : bcftools query -H -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER AF=[%AF]\t \n' normal1.vcf.gz > filtered.vcf
    and then i added the header to this file and filtered bialleles by select variants.

    Command used for generating Calculate Contamination
    java -jar /PathToGatk CalculateContamination
    -I tumor_getpileupsummaries.table
    -tumor-segmentation segments.table
    -O tumor_calculatecontamination.table

    OUTPUT (segments.table)
    #<METADATA>SAMPLE=Hg19_P1
    contig start end minor_allele_fraction

    OUTPUT (tumor_calculatecontamination.table)
    sample contamination error
    Hg19_P1 NaN 1.0

    I am stuck at this, no values are comming, except 0.

    can you guide me with this issue @bhanuGandham
  • RishabhRishabh IndiaMember
    @bshifaw
    Thankyou for reply
    I looked the documents provided by you ,but it's still not resolved, can you suggest some other thing.
  • bshifawbshifaw Member, Broadie, Moderator admin

    Running CalculateContamination using the following jar file resulted in the same issue?
    contamination-patch-5-27-2019.jar

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