Question: Meaning of Pindel RefSupportingLeft and RefSupportingRight output
gravatar for rocco.piazza
2.2 years ago by
rocco.piazza0 wrote:


I am having trouble interpreting the Pindel "per sample" columns of the output files. In a previous post it has been reported that 32+ data are sample Id plus 6 values indicating: 1) RefSupportingLeft 2) RefSupportingRight 3) AltSupportingLeft 4) AltSupportingLeftUnique 5) AltSupportingRight 6) AltSupportingRightUnique

and that you should take max(RefSupportingLeft, RefSupportingRight) and sum(AltSupportingLeft, AltSupportingRight) to get your genotype.

This is a bit confusing because apparently these data don't fit with what is reported in IGV (aligner is BWA). The major issue is that the number of 'reference' counts doesn't match with ref read counts shown in the viewer. Could anyone explain in detail how the RefSupportingLeft and RefSupportingRight are calculated ?

Thanks, Rocco

ADD COMMENTlink written 2.2 years ago by rocco.piazza0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2084 users visited in the last hour