Hi there. So I'm working with paired sam/bam files, filtering and subsetting them. I have noticed in some step of the filtering I have lost the flag "properly paired" when checking with samtools flagstat. And apparently a software (danpos) is requiring this field in samtools flagstat to be filled.
Is there any way to manually add it? Made a quick look but didn't find anything. I know that they are properly paired because they are coming from a a larger bam file with all properly paired-reads... So I'm getting this from samtools flagstat:
7261380 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 7261380 + 0 mapped (100.00% : N/A) 7261380 + 0 paired in sequencing 3630690 + 0 read1 3630690 + 0 read2 0 + 0 properly paired (0.00% : N/A) 7261380 + 0 with itself and mate mapped 0 + 0 singletons (0.00% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
And I would like to get also 7261380 as properly paired.
Thanks for your feedback!