MAPQ = 60 is compulsory for the whole of GATK pipeline
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.