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Hello,
I am having trouble interpreting the Pindel "per sample" columns of the output files.
In a previous post it has been reported that lines 32+ 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 for two reasons:
1) Apparently these data don't fit with what I see in IGV (aligner is BWA; IGV downsample reads function and filters have been disables). The major issue is that the number of 'reference' counts doesn't match with ref read counts shown in the viewer.
2) Why we should take MAX of RefSupporting and SUM of AltSupporting to generate the correct genotype ?
All the best,
Rocco
I am having trouble interpreting the Pindel "per sample" columns of the output files.
In a previous post it has been reported that lines 32+ 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 for two reasons:
1) Apparently these data don't fit with what I see in IGV (aligner is BWA; IGV downsample reads function and filters have been disables). The major issue is that the number of 'reference' counts doesn't match with ref read counts shown in the viewer.
2) Why we should take MAX of RefSupporting and SUM of AltSupporting to generate the correct genotype ?
All the best,
Rocco