samtools rmdup PE

[m_elena_bioinfo]

Hi users,
someone knows what is the difference between:
>samtools rmdup
and
>samtools rmdup -S.

They remove PCR duplicates in paired end data, and the tutorial says that -S option it's useful to treat PE reads as single-end data.

I run both the script and, starting from a 750Mb bam file, I generated 650Mb bam file (without using -S option) and 350Mb bam file (using -S option).

Thanx a lot!
ME

[CowGirl]

RmDup with the -S option

I have a similar question - what exactly does "-S" do with paired end reads?

[swbarnes2]

If you have one pair of reads where read 1 starts at position 100, and the other end starts at position 200, and a second pair of reads where read 1 starts at position 100, and read 2 starts at position 250, those came from different fragments of DNA. You can tell because the read 2 start is different, even though the read 1 start is the same.

When treating the reads as paired end, none of those reads should be deleted as PCR duplicates.

However, if you ran rmdup -S, the software will not check to see if read 2 has a different start coordinate, so one of those read 1 reads will be treated as a duplicate, and deleted.

[CowGirl]

Hi swbarnes2, thanks for the reply. That makes more sense than all the answers I've found as of yet!