Discrepancy between sambamba and samtools

[sybrohee]

Dear all,

I discovered a discrepancy when counting the reads between samtools and sambamba

samtools view -c -L file.bed file.bam and sambamba view -c -L file.bed file.bam

Apparently, when counting the reads, sambamba filters out reads that are unaligned but that have their mate paired AND where the aligned mate starting alignment position corresponds to one starting position in the bed file +1.

Is this a bug in sambamba (or in samtools) or is there a way to circumvent the issue?

samtools 1.7 sambamba 0.6.7-pre1

[pjotrp]

Handling of bed files is slightly different, see other issues on the tracker.

[pjotrp]

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