I research rare mendelian diseases and generally look for shared variants between my related affected samples. Because of variation in the quality and coverage of exomes, I want to be able to look at a merged variant file for all of my affected cases.
This is relatively straight forward with vcf tools however if for example I am looking at the shared variants of two individuals, some variants may not be shared because of three reasons: 1. one individual has variant allele and one has wild-type i.e. not shared. 2) variant not covered on second exome 3) variant covered on second exome but at allele frequency below cutoff for variant call.
Can anyone help with a method to annotate the merged variant list with the depth and allele call for each of the samples including calling the wild-type allele where true.
p.s I had thought of using bedtools to annotate the depth of read at each start position but this wouldnt help me annotate with wildtype calls.
Thanks
Josh
This is relatively straight forward with vcf tools however if for example I am looking at the shared variants of two individuals, some variants may not be shared because of three reasons: 1. one individual has variant allele and one has wild-type i.e. not shared. 2) variant not covered on second exome 3) variant covered on second exome but at allele frequency below cutoff for variant call.
Can anyone help with a method to annotate the merged variant list with the depth and allele call for each of the samples including calling the wild-type allele where true.
p.s I had thought of using bedtools to annotate the depth of read at each start position but this wouldnt help me annotate with wildtype calls.
Thanks
Josh
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