View Single Post
Old 07-04-2013, 09:30 AM   #54
smapdy
Junior Member
 
Location: California

Join Date: Mar 2011
Posts: 3
Default

Thanks for the reply valeu. I can't use the hg19 file because my exomes are from mice. I downloaded and generated a SNP file that, I believe, matches the formatting of the human files:

chr1 3000568 A/G + T rs29444956
chr1 3000621 A/C + C rs31439779
chr1 3001490 A/C + C rs31521921
chr1 3001579 A/T + A rs30468828
chr1 3001712 C/G + C rs32793997
chr1 3003268 A/G + A rs30748911
chr1 3003414 A/G + A rs31953890
chr1 3003449 C/T + T rs32186899
chr1 3003464 A/G + G rs31079645
chr1 3003508 C/T + C rs32044173


My .pileup files are formatted as follows:

chr1 3216016 T 44 ......................,.........,..,,,...,^].^];=>>?>?<=??>>???>=>?>>??>>??>>>>@=>?<<::=;<<
chr1 3216017 G 45 ......................,.........,..,,,...,..^].=@@ACCC?ACC@ACCC<BAAB5?CCBCCAAABAAB?:?>?=;?><
chr1 3216018 T 47 ......................,.........,..,,,...,...^].^], :9?=>@9==@>>>@>?=><@>=<==>@?>>=?>>?=;<===9;;;<9
chr1 3216019 A 48 .$.....................,.........,..,,,...,....,^]. 99><<??3<??<<???<<;><<<=?=?><<<>?>>=8<<<=6;:9;:<
chr1 3216020 T 47 .....................,.........,..,,,...,....,.:==???<=?>==???===?=4?<?=??===?@>??<??=?>=;;:;<


I believe this is standard .pileup format. Despite appearances both of the above are actually tab-delimited.

In the event that I can't get BAF calculation to work, what is are the repercussions? I know there are a few options which are explicitly dependent upon BAF (like noisyData). How much will it impact the analysis if these options are disabled?
smapdy is offline   Reply With Quote