Vcf file with 3 samples and trying to count variants

Question

[kadamek49]

Hello,

I have a vcf file with 3 samples from the same plant (bot, mid, top sections were sequenced) and I am trying to look into any accumulated mutations that were possibly carried on from the bottom to top samples. I was able to find the number of ALT for each sample independently with the code below but I am struggling to find the accumulation. I am looking for mutations counts occurring in sample1+sample2 (bot+mid), sample2+3 (mid+top), sample1+2+3 (bot+mid+top). Any help would be greatly appreciated. Thank you.

$ java -jar dist/bioalcidaejdk.jar  -e 'stream().flatMap(V->V.getGenotypes().stream().filter(G->G.isCalled()&&!G.isHomRef()).map(G->V.getContig()+"\t"+G.getSampleName())).collect(Collectors.groupingBy(Function.identity(),Collectors.counting())).forEach((K,C)->println(K+":"+C));'  example.vcf