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avg_depth_per_target from DiagnoseTarget and DepthOfCoverage

sgoyalsgoyal San CarlosMember

Calculated avg depth per target from DiagnoseTarget and DepthOfCoverage tools, they gave different numbers.
DiagnoseTarget number are lower, why ?
Calculated avg coverage from per loci file generate by DepthOfCoverage too.. it complies with its avg depth

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Thanks.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sgoyal
    Hi,

    Can you post the exact commands you ran and confirm you are using the latest version of GATK?

    Also, please post an example where the two outputs differ.

    Thanks,
    Sheila

  • sgoyalsgoyal San CarlosMember

    Using GATK 3.5

    java -jar GenomeAnalysisTK.jar \
    -T DepthOfCoverage \
    -R reference.fasta \
    -o file_name_base \
    -I input_bams.list
    -L my_capture_genes.interval_list

    Example from DOR output (interval summary file)---

    Target total_coverage average_coverage E1_total_cvg E1_mean_cvg E1_granular_Q1 E1_granular_median E1_granular_Q3 E1_%_above_15
    chr6:65017013-65017133 155350 1283.88 155350 1283.88 >500 >500 >500 100

    java -jar GenomeAnalysisTK.jar
    -T DiagnoseTargets \
    -R reference.fasta \
    -I sample1.bam \
    -L intervals.interval_list \
    -o output.vcf

    Example from diagnose target output---

    chr6 65017013 . C

    . PASS END=65017133;IDP=1171.40;IGC=0.273 IDP:LL:ZL 1171.40:0:0
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sgoyal
    Hi,

    I am wondering if the different input BAMs are different. I think you put in a lot of BAMs in the first command, but in the second command, you only put one in. Can you try running on the exact same BAM for both?

    Thanks,
    Sheila

  • sgoyalsgoyal San CarlosMember

    They were same bams. I am running another set now, will update if i see difference again

  • sgoyalsgoyal San CarlosMember

    ok, i checked with multiple bams.. average depth reported by both tools are different. can you please do quick check at your end with some sample file

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sgoyal
    Hi,

    It looks like DiagnoseTargets does not count reads that have low quality, but DepthOfCoverage does. However, if you set -BQ to 0, you should get the same results :smile:

    -Sheila

  • sgoyalsgoyal San CarlosMember
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