I have a multi-sample vcf file and I want to get a table of IDs on the left column with the variants in which they have an alternate allele in. It should look like this:

> ID1 chr2:87432:A:T_0/1 chr10:43234:C:G_1/1  
ID2 chr2:87432_A:T_1/1   
> ID3 chr11:432434:T:G chr14:34234234:C:G chr20:34324234:T:C

This is to then read into R

I have tried combinations of:

    bcftools query -f '[%SAMPLE\t] %CHROM:%POS:%REF:%ALT[%GT]\n'

but I keep getting sample IDs overlapping on the same line and I can't quite figure out the sytnax.

Your help would be much appreciated
something like a loop over each sample:

```
bcftools query -l in.vcf.gz | while read S; do echo -n "$S" && bcftools view --samples $S -O u in.vcf.gz | bcftools query  -i 'AC>0'  -f '\t%CHROM:%POS:[%GT]' && echo ; done
```

I'm too lazy to convert the alleles' indexes to their value...