possorted_bam.bam versus phased_possorted_bam.bam

[burrir]

Hi,
I would be curious to hear whether you expect the possorted_bam.bam output by "LongRanger align" (rather than the phased_possorted_bam.bam output by "LongRanter wgs") should work adequately in linkedSV?

We are looking to replace LongRanger wgs, as it is tremendously time consuming, and to our understanding, LongRanger align provides a phased output as well. We yet fail to understand the difference between the bam files output by the two different pipelines.

Any insights would be very appreciated!

Best wishes,
Reto

[fangli80]

Hello Reto,
Yes. I understand that the Longranger pipeline is pretty slow.
I have not tested on the "possorted_bam.bam". Does the bam file has a "BX" tag for barcode and an "HP" tag for haplotype?

Thanks,
Li

[burrir]

Hi Li,

thanks a lot for getting back on this question! The merely possorted bam files contain the BX field. This is what e.g. hapCUT2 uses to infer phase information (which is why I figured that there is phase info, but it's the info to infer phase and not phase info itself). However, as I now saw when checking, these files do not feature the HP tag. Thus the difference in naming and why using the possorted_bam will not work for linkedSV.

Thanks again & best wishes!
Reto