AlignmentSieve returns empty bam file

[gdolsten]

Hi, I am trying to use alignmentSieve to shift some reads in a BAM file. I am trying the following command using deeptools 3.5.0:

alignmentSieve -b sorted.test.bam -o sieve.sorted.test.bam --shift 10 10

But the output file, sieve.sorted.test.bam has no output. The input file is fine, and if I remove the --shift argument, the two files are now identical. How can I figure out what is going on here?

[dpryan79]

The most likely cause is that you have no proper pairs. Improper pairs are filtered out, since there's no coherent way to shift the resulting fragments.