MAPQ = 60 is compulsory for the whole of GATK pipeline

lovehardwarelovehardware AustraliaMember

Hi GATK team
I am using GATK pipelines for Calling Variant from RNA seq data. However I am using now TopHat instead of STAR because of my limited PC power (just 8 core + 16 GB).Because of using TopHat2, myMAPQ score seem to have value of 0, 1, 3 and 50. And I know that 50 assign for unique map. My question is if I should transfer from score 50 to default score 60 as described in the GATK pipeline as following

java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R /homeref.fasta -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 50 -RMQT 60 -U ALLOW_N_CIGAR_READS (replace 255 by 50)

OR if I could keep score 50 for steps ahead?

Thank you very much for your consideration.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Using TopHat's MAPQ 50 scores should be fine; the base requirement is that uniquely mapped reads must have a MAPQ value that is in the usable range. We assign 60 arbitrarily, but 50 should work just as well.

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