AutoQC Properly Paired check is not checking properly paired flag

[mp15]

The check at:
https://github.com/VertebrateResequencing/vr-pipe/blob/master/modules/VRPipe/Steps/vrtrack_auto_qc.pm#L250
is wrong. Properly paired is a flag on BAMs and given that bamcheck does not calculate it then this must be incorrect.

[sb10]

The value it's actually calculating seems to be percent of all reads mapped that were not duplicates.

Is the fix simply to update the name of the test to make it clear what the value really is?

Should an additional test be added later to give the real properly paired stat once we switch to using 'samtools stats' (and after your samtools request #106 is pulled)?

[sb10]

Oh, there is already a 'duplicate reads' stat calculated that is just the inverse of this. So the fix should be to get the correct properly paired value from samtools stats, once 106 is pulled. In the mean time we'll just leave things as they are.

[mp15]

Aye that was what I was thinking. I think Petr is waiting on your input before merging #106 so you might want to have a chat with him.

On 6 Jan 2014, at 11:12, Sendu Bala [email protected] wrote:

Oh, there is already a 'duplicate reads' stat calculated that is just the inverse of this. So the fix should be to get the correct properly paired value from samtools stats, once 106 is pulled. In the mean time we'll just leave things as they are.

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[sb10]

Was this ever resolved?

[mp15]

The bamcheck parser fix was done in august 2014 by ddc621b however this fix was never incorporated into autoqc:
https://github.com/VertebrateResequencing/vr-pipe/blob/master/modules/VRPipe/Steps/vrtrack_auto_qc.pm#L277