Hi,

I have multi-sample vcf and in this vcf, there are many sites which have uncalled or missing genotype. Is there a way to check which sample has greater number of uncalled genotypes in vcf. So that I can exclude that sample from further analysis.
A one liner using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

    $ java -jar dist/bioalcidaejdk.jar -e 'stream().flatMap(G->G.getGenotypes().stream()).filter(G->!G.isCalled()).map(G->G.getSampleName()).collect(Collectors.groupingBy(Function.identity(), Collectors.counting())).forEach((K,V)->println(K+"\t"+V));' src/test/resources/test_vcf01.vcf  | sort -t $'\t' -k2,2n

    
    
    S3	8
    S4	9
    S5	14
    S6	18
    S2	23
    S1	73


  * `stream(). `get a stream of variants
  * `flatMap(G->G.getGenotypes().stream()).` map to a stream of genotypes
  * `filter(G->!G.isCalled()).` keep the uncalled genotype
  * `map(G->G.getSampleName()). ` map to the sample name
  * `collect(Collectors.groupingBy(Function.identity(), Collectors.counting())) ` convert to associative array sample/count
  * .`forEach((K,V)->println(K+"\t"+V)); ` print the results.