biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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proper_pair not the same as -f 0x2 #401

Closed mictadlo closed 4 years ago

mictadlo commented 5 years ago

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

What did I miss?

Thank you in advance,

Michal