Describe the bug
I am currently using pbmm2 align to map my subreads bam to hg38. I got chimeric reads by using 'grep "SA:Z:". But i found that pbmm2 gives many alignments for one reads. The mapped position of these reads just show a few or dozens of bases apart, but have different mapq values, and more than one has a mapq of 60. How can I find the best hits for further analysis?
For example:
Operating system linux
Package name pbmm2 1.13.0
Using: pbmm2 : 1.13.0 (commit v1.13.0-2-gbcd99f5) pbbam : 2.4.99 (commit v2.4.0-23-g59248fe) pbcopper : 2.3.99 (commit v2.3.0-28-ga9b1ffa) boost : 1.81 htslib : 1.17 minimap2 : 2.26 zlib : 1.2.13
Describe the bug I am currently using pbmm2 align to map my subreads bam to hg38. I got chimeric reads by using 'grep "SA:Z:". But i found that pbmm2 gives many alignments for one reads. The mapped position of these reads just show a few or dozens of bases apart, but have different mapq values, and more than one has a mapq of 60. How can I find the best hits for further analysis? For example:
To Reproduce
pbmm2 align /public1/data/heke/pacbio/hg38_noalt.mmi subreads/m64032_190605_101534.subreads.bam /public1/data/heke/pacbio/mapping/test/noalt_aligned.m64032_190605_101534.subreads.bam --preset SUBREAD --median-filter