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GATK4: How to reassign STAR mapping quality from 255 to 60 with SplitNCigarReads
How can I reassign STAR mapping quality from 255 to 60 with SplitNCigarReads?
In GATK 3.X this used to be done like this:
java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ref.fasta -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
See this blog post: https://software.broadinstitute.org/gatk/blog?id=4285
With GATK4 latest beta the read filter argument has been renamed. Trying the same
-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS arguments leads to the following error:
A USER ERROR has occurred: rf is not a recognized option
Trough looking at the CLI help documentation I got as far as:
--readFilter ReassignOneMappingQuality -RMQF 255 -RMQT 60
The readFilter argument is now recognized. But not the
-RMQF 255 -RMQT 60 part:
A USER ERROR has occurred: U is not a recognized option
Could you please advice on how to run the GATK4 SplitNCigarReads tool with reassignment of the mapping quailty?
Without reassignment of the mapping quality GATK haplotype caller discards all the STAR mapped reads, and calls full chromosome reference, without any variant.