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Question regarding calling denovo mutations
In the genotype refinement process at the last step, 'hiConfDenovo' and 'loConfDenovo' mutations are tagged.
After Genotype Refinement, I just filtered 'hiConfDenovo' mutations in the separate VCF file by SelectVariants. But i have confusion regarding the results when i looked at the genotypes information of individuals from trios.
I just want to know how the following Genotype is called denovo for the affected child (male)? My data set was unphased when i process it through genotype refinement protocol.
GT:AD:DP:GQ:JL:JP:PL:PP (child) 0/1:202,15:223:86:6:40:89,0,711:86,0,761 (father) 0/0:235,8:248:43:6:40:0,42,891:0,43,900 (mother) 0/1:226,10:236:46:6:40:6,0,665:46,0,673 (REF= C, ALT=A)
GT:AD:DP:GQ:JL:JP:PL:PP (child) 0/1:16,12:28:99:52:52:231,0,428:291,0,485 (father) 0/0:24,1:25:58:52:52:0,66,732:0,58,775 (mother) 1/1:2,26:29:55:52:52:730,53,0:798,55,0 (REF= A, ALT=G)
GT:AD:DP:GQ:JL:JP:PL:PP (child) 0/1:15,10:25:99:75:75:263,0,377:263,0,443 (father) 0/1:20,8:29:99:75:75:183,0,572:243,0,578 (mother) 0/0:27,0:27:75:75:75:0,75,850:0,75,856 (REF= C, ALT=T)
The child can inherit from father or mother the respective alleles, so how can we call that de novo mutation for affected child? Also these two SNPs are already existed in dbSNP database.. That is mentioned in VCF file.
I am pretty new in this field, Can you please clear this?