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Service note: Geraldine is on vacation this week; other members of GSA will be responding to questions, but they have a lot of work besides this, so be aware that responses may be a little slower than usual. Thank you for your patience.

Not printed BQ tags in the bam file after recalibration.

saharsahar Posts: 1Member ✭
in Ask the team

Hi all; I use the old version of GATK and it seems that -T TableRecalibration does not work correctly on my .bam file. Nothing is printed out as BQ tag although I use these parameters:

    java -Xms5g -Xmx5g -jar $GATK/GenomeAnalysisTK.jar \
    -R $REF \
    -I $d/$f\_marked.bam  \
    -o $d/$f\_recalibrated.bam \
    -T TableRecalibration \
    -baq RECALCULATE \
    --doNotWriteOriginalQuals \
    -recalFile $d/$f\_marked.bam.csv \
    -et NO_ET

I would appreciate any input.

Post edited by Geraldine_VdAuwera on
Tagged:
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