What is the samtools flag used in bamPEFragment?

Question

[Soohyun]

I want to know samtools flag used in bamPEFragment.

[Pierre Lindenbaum]

what is bamPEFragment ?

[GenoMax]

Possibly this command from deepTools: https://deeptools.readthedocs.io/en/develop/content/tools/bamPEFragmentSize.html

[Soohyun]

Select read in bamPEFragment using the conditions below. What is the flag in samtools for the conditions below?

reads = np.array([(abs(r.template_length), r.infer_query_length(always=False))
                          for r in bam.fetch(chrom, start, end)
                          if r.is_proper_pair and r.is_read1 and not r.is_unmapped])

[GenoMax]

Flag is probably 66. You can find the SAM/BAM flags by using this helpful page: https://broadinstitute.github.io/picard/explain-flags.html