I am looking for a pathogenic variant with exome sequencing on affected and unaffected related individuals. Initial analysis has not shown any obvious candidates. Im looking to retrieve more information with our existing data set which might support or refute different genome regions. It is a relatively small population. I would expect that the pathogenic variant is probably linked to several other variants based on the limited number of potential cross-over events that separate the individuals. GATK was used to call variants and I know that phased allele information is in our vcf files. I am struggling to interpret the annotation. Is there a way to select or filter variants based on shared linkage or do I need to manually inspect variants to retrieve that information?
Any advice would be greatly appreciated. Thank you