I have a multisample vcf file (3 samples) and I'd like to get all denovo variants for a specific sample. I tried bcftools:
bcftools view -s SAMPLE_ID -x All-final.vcf
The problem is, that some sites can be multiallelic. So the above command would e.g. not find this line (The third sample is the one I'm interested in):
chr5 38528951 rs762238623 GACAC GAC,G 1204.93 PASS . GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:2,6,0:2:75:6,0:212,0:-15.9529,0,-3.87444,-16.555,-5.68062,-22.6541 0/1:40:10,21,3:10:343:21,3:677,105:-51.4565,0,-21.4531,-45.9266,-19.2432,-72.8601 1/2:39:0,19,10:0:0:19,10:622,279:-72.2747,-22.0435,-16.3239,-50.201,0,-47.1907
Because the requirements are not fullfilled:
-x, --private print sites where only the subset samples carry an non-reference allele. Requires --samples or --samples-file.
So, what's the best way here to find all denovo variants in a given sample?