`

过滤掉 secondary_alignment or supplementary

sambamba view -q -f bam --filter='not (secondary_alignment or supplementary)' xxxx.minimap2.hg19.xxx.bam > xxx.minimap2.hg19.chr10.primary_aln.nosupp.bam
`

`

过滤质量只低于20的,指定区域

sambamba view -q -f bam --filter='mapping_quality >20' x.minimap2.hg19.bam 10:1-1234567 > xx.bam
or
samtools view -b -m 20 x.minimap2.hg19.bam 10:1-1234567 > xx.bam
`

参考
https://github.com/biod/sambamba/wiki/[sambamba-view]-Filter-expression-syntax
https://broadinstitute.github.io/picard/explain-flags.html