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UG outputs VCFs where different lanes from same sample are treated as separate individuals

PihlstromPihlstrom Posts: 9Member

Dear Team,

We are running an exome sequencing project where we have sequenced samples on two different lanes. Aligning with bwa, we assign identical ID and SM tags, yet different PU tag for these files. This should be in line with your general recommendations, keeping the lane information available for recalibration purposes. We have then fed both files from the same sample into the base recalibration step to create a common, sample-level bam, also in accordance with recommendations previously posted on the forum. However, when calling variants we get VCFs where UnifiedGenotyper has treated the different lanes as separate samples. What are we doing wrong? Is this approach not possible after all, so an identical read group is required for each sample?

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  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,869Administrator, GATK Developer admin

    In principle you're doing the right thing -- UG should be grouping data based on SM tag. Can you post the read group info and the header line of the VCF (showing the titles of the columns) so we can have a look at what's going on there?

    Geraldine Van der Auwera, PhD

  • PihlstromPihlstrom Posts: 9Member
    edited November 2013

    Shure!

    The bwa commands used to add read group info in the alignment step looked like this:

    bwa sampe -r '@RG\tID:RHEX1\tPL:ILLUMINA\tSM:RHEX1\PU:lane2'

    bwa sampe -r '@RG\tID:RHEX1\tPL:ILLUMINA\tSM:RHEX1\PU:lane1'

    And the columns in the VCF come out like this:

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RHEX1U:lane1 RHEX1U:lane2

    (Don't know why the text above came out in such huge letters...)

    Best regards, LP

    Post edited by Pihlstrom on
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