#11 Syn-Nonsyn-at-position not compatible with subsampled pileups, nor overlapping genes

[Anonymous]

Originally created by: maryro... (code.google.com)@gmail.com

Great software you have developed here!

I just wanted to raise awareness of a couple issues I have come across in my analyses:

1. The syn-nonsyn-at-position.pl script will not accept a sub-sampled pileup as its input pileup file. If this can be easily solved I would love to extract the information generated for another analysis - however, I have found that the analysis is very sensitive to coverage differences hence my desire to use sub-sampled pileups.

2. I have found that SNPs landing in greater than one gene are not annotated. This is not really a problem for me, as I can extract this information myself, but I thought I would mention it in case someone else has been perplexed by the phenomena.

[Anonymous]

Originally posted by: RoKof... (code.google.com)@gmail.com

many thanks for this issues!
- What error message do you get when you use the subsampled pileup?
- at point two you mean that the snp is present in several  overlapping genes?

[Anonymous]

Originally posted by: maryro... (code.google.com)@gmail.com

Sorry for my delayed response! I am revisiting my prior analyses and for issue #1 I am no longer having a problem using a sub-sampled pileup. I am guessing it was a user error on my part. For issue #2, yes, I mean that the SNP is present in several overlapping genes. I have not revisited this part of my prior analyses yet, but will report back if I find something more.