Hi
It appears that proper_pair does not deliver the same results as -f 0x2
> sambamba view -h -t 2 -F "not (unmapped or secondary_alignment) and not duplicate and [XS] == null and mapping_quality >= 30 and proper_pair" SRR1043177.fastp.fastq.gz-hisat2.sorted.bam | wc -l
32102628
> sambamba view -h -t 2 -F "not (unmapped or secondary_alignment) and not duplicate and [XS] == null and mapping_quality >= 30" SRR1043177.fastp.fastq.gz-hisat2.sorted.bam | samtools view -f 0x2 - | wc -l
32102605
Hi It appears that proper_pair does not deliver the same results as -f 0x2
What did I miss?
Thank you in advance,
Michal