[STAR] 255 Mapping Quality

Question

[umn_bist]

So STAR aligner has an option, by default, (--outSAMmapqUnique) to assign 255 as MQ for unique mappers.

${STAR} --runMode alignReads \
        --twopassMode Basic \
        --runThreadN 24 \
        --outSAMtype BAM SortedByCoordinate \
        --outSAMattributes All \
        --outFileNamePrefix "${file1%_1.fastq}_tsta" \
        --outSAMmapqUnique 255 \
        --sjdbGTFfile "${sjdb}" \
        --genomeDir "${STAR_index}" \
        --readFilesIn "${file7}" "${file8}"

I had overlooked this and, from my guess, is causing majority of my reads to be filtered using GATK MuTect2:

java -jar -Xmx32g ${GATK} MuTect2 \
        -R "${reference}" \
        -I:tumor "${inpT}" \
        -I:normal "${inpN}" \
        --dbsnp "${dbSNP_1}" \
        --cosmic "${COSMIC_1}" \
        -L "${interval}" \
        --filter_reads_with_N_cigar \
        --out "${varCall}"

Result:

MicroScheduler - 18076 reads were filtered out during the traversal out of approximately 18167 total reads (99.50%)
MicroScheduler --> 0 reads (0.00% of total) failing BadCigarFilter
MicroScheduler --> 1601 reads (8.81% of total) failing DuplicateReadFilter
MicroScheduler --> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
MicroScheduler --> 11 reads (0.06% of total) failing MalformedReadFilter
MicroScheduler --> 16384 reads (90.19% of total) failing MappingQualityUnavailableFilter
MicroScheduler --> 80 reads (0.44% of total) failing NotPrimaryAlignmentFilter
MicroScheduler --> 0 reads (0.00% of total) failing UnmappedReadFilter

I am wondering, when calling variants, for each read base, there is a unique MQ assigned? If so is there a way to preserve MQ for each of them? Is this as simple as removing --outSAMmapqUnique filter? I'd prefer not to reassign them all to 60 as I would like to select variants against MQ for annotations.

As always, thank you for your time and help.

EDIT: Interesting bit from GATK:

At this step we also add one important tweak: we need to reassign mapping qualities, because STAR assigns good alignments a MAPQ of 255 (which technically means "unknown" and is therefore meaningless to GATK). So we use the GATK's ReassignOneMappingQuality read filter to reassign all good alignments to the default value of 60. This is not ideal, and we hope that in the future RNAseq mappers will emit meaningful quality scores, but in the meantime this is the best we can do. In practice we do this by adding the ReassignOneMappingQuality read filter to the splitter command.

I know there is a way to assign unique mapper to 60 in STAR so this may be my only option. Is this still an issue with RNA-seq aligners - not preserving/assigning meaningful MQ scores? Does TopHat2 run into this issue?

[prasundutta87]

HISAT2 (v2.0.4 definitely and probably the current version too) assigns the score of 60 to unique mappers..

Answer 1

[zeyuchen2016]

I don't know whether your issue have been solved.

you could see this blog