Almost exclusive "G" or "g" output

[timothee-revil]

Hi,

The output from pileup2baseindel.pl is giving me almost exclusively "G" or "g".

Example:

chr1 6610726 C 0 0 0 74 0 0 0 0 NA NA
chr1 6610727 T 0 0 0 73 0 0 0 0 NA NA
chr1 6610728 G 0 0 0 88 0 0 0 0 NA NA
chr1 6610729 A 0 1 0 87 0 0 0 0 NA NA
chr1 6610730 A 0 0 1 87 0 0 0 0 NA NA
chr1 6610823 a 0 0 0 0 0 0 0 82 NA NA
chr1 6610824 a 0 0 0 0 0 1 0 81 NA NA
chr1 6610825 c 0 0 0 0 0 0 0 84 NA NA
chr1 6610826 c 0 0 0 0 0 0 0 49 NA NA
chr1 6610827 t 0 0 0 0 0 0 0 49 NA NA

Command used:
perl pileup2baseindel.pl -i ../alignedBAMs/GermLine_gDNA.pileup -prefix Germline

Am I doing something wrong? I'd love to get this script to work, it's exactly what I need for a project.

Thanks for your time,
Tim

[riverlee]

Could you share the GermLine_gDNA.pileup so I can take a look? Thanks

Jiang

[timothee-revil]

Sure, I've extracted just the chr17 for a smaller file size. I checked and get the same results (Gs).

https://www.dropbox.com/s/n1atqtgz4zkw4n4/Germline.chr17.pileup?dl=0

Thanks!
Tim

[sfbrunner]

I am having the same issue. Has this been resolved?

[mWekking]

I know this is a long shot, but I also have this problem.... any solutions?? when using the no_strand.pl version, everything works fine ...