Output allele of the normal sample

[fredsamhaak]

Hi @litaifang,

Thanks for your great tool which helps me a lot.
I wonder if there is an option/parameter to output the vcf file which contains not only the allele of tumor sample but also the normal sample. For example:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO        FORMAT  Patient_01_Germline Patient_01_Somatic
1   69091   .   A   C,G .       PASS    AF=0.1122   GT      1/0                 2/1
1   69849   .   G   A,C .       PASS    AF=0.1122   GT      1/0                 2/1
1   69511   .   A   C,G .       PASS    AF=0.3580   GT      1/1                 2/2

As you can see from the above example, for chr1:69091, reference genome is 'A', germline(normal sample) is 'C' and somatic(tumor sample) is 'G'.

It is the right thing to use this kind of format to annotate cancer samples with tools like SnpEff since we actually want to know what would happen when 'C' change into 'G' (normal vs. tumor) instead of 'A'-->'G' (ref vs. tumor), but I struggle dealing with this problem and still have no idea.

I will be very grateful if you can give me some advice! And thanks in advance.

All the best,
He

[litaifang]

SomaticSeq's GT annotation isn't very sophisticated.
How was that VCF format obtained? From which tool? I don't think SomaticSeq would put germline variant and somatic variant in the same ALT field.

[fredsamhaak]

Hi @litaifang, for now I don't find tools which would output that kind of VCF format but SnpEff ask for that (pls check it from here) when annotating cancer samples for somatic variants, which seems reasonable.
Do you have any ideas or suggestions about it? Thank you Li Tai.

All the best,
He