View Single Post
Old 08-27-2014, 04:57 AM   #5
thek71
Junior Member
 
Location: Freiburg

Join Date: Mar 2011
Posts: 4
Default

Hi all,
I have a similar question regarding the germline mutations. I have several tumor-normal samples for which I have used the somatic command and I want to check several genes for germline mutations. From the publication is stated that hc variants are the ones with at least 10% allele frequency in normal and tumor samples.
This varinat is in the hc file:
chr1 565088 C T 0 37 100% T 4 19 82.61% T Germline 1.0 0.018159073897484498 2 2 10 9 0 0 22 15
while this one
chr1 741267 T C 33 38 53.52% Y 30 22 42.31% Y Germline 5.540944545408712E-23 0.9211526256316275 2 28 3 19 10 23 5
33
is not. The numbers of reads and the percentages seem to be ok, but I fail to understand why the variants are categorized differently.
Any help would be highly appreciated.

Thank you in advance
thek71 is offline   Reply With Quote