Hi,

I've used freebayes for calling variants on a set of bamfiles with 1 sample in each bam file. 
I want to somehow get a good overview over the variants that also non-bioinformaticians can look at.

The VCF file looks something like this: 

    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 CONTROL
    chr1       46      .       ACACC   CCACA   8.58901e-15     .       AB=0;ABP=0;AC=0;AF=0;AN=5;AO=2;CIGAR=1X3M1X;DP=137;DPB=147;DPRA=0.314961;EPP=3.0103;EPPR=17.5948;GTI=0;LEN=5;MEANALT=1;MQM=33;MQMR=54.4254;NS=5;NUMALT=1;ODDS=78.0575;PAIRED=1;PAIREDR=0.977612;PAO=0;PQA=0;PQR=506;PRO=17;QA=14;QR=4464;RO=134;RPP=7.35324;RPPR=77.9423;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=83;SRP=19.6042;SRR=51;TYPE=complex;technology.ILLUMINA_HiSeq2500=1    GT:DP:RO:QR:AO:QA:GL    0:81:80:2614:0:0:0,-10  0:6:6:218:0:0:0,-10     0:10:8:262:2:14:0,-10   0:19:19:671:0:0:0,-10   0:21:21:699:0:0:0,-10
    chr1       2146    .       G       A       9.16135e-15     .       AB=0;ABP=0;AC=0;AF=0;AN=5;AO=28;CIGAR=1X;DP=251;DPB=251;DPRA=0;EPP=5.80219;EPPR=11.1996;GTI=0;LEN=1;MEANALT=1;MQM=18.9643;MQMR=57.3318;NS=5;NUMALT=1;ODDS=92.9516;PAIRED=0.964286;PAIREDR=0.977578;PAO=0;PQA=0;PQR=0;PRO=0;QA=633;QR=8052;RO=223;RPP=63.8115;RPPR=5.82445;RUN=1;SAF=11;SAP=5.80219;SAR=17;SRF=99;SRP=9.09627;SRR=124;TYPE=snp;technology.ILLUMINA_HiSeq2500=1   GT:DP:RO:QR:AO:QA:GL    0:145:136:4920:9:154:0,-10      0:27:22:788:5:129:0,-10 0:16:13:471:3:75:0,-10  0:13:9:333:4:100:0,-10  0:50:43:1540:7:175:0,-10


I've tried using both gatk and snpsifts variantotable/extractfields tools, but it will only sum all the INFO counts and not keep them separated. 

My goal is to get something like this: 
    
    CHR POS EFF.FIELD1 REF ALT QUAL SAMPLE1.RO SAMPLE1.AO SAMPLE2.RO SAMPLE2.AO SAMPLE3.RO SAMPLE3.AO SAMPLE4.RO SAMPLE4.AO CONTROL.RO CONTROL.AO
    chr1 46 "geneX" ACACC CCACA 8.58901e-15 80 0 6 0 8 2 19 0 21 0 

But the current options would give something like: 

     CHR POS EFF.FIELD1 REF ALT QUAL RO AO
     chr1 46 "geneX" ACACC CCACA 8.58901e- 134 2

My feeling is that this should be fairly common, so just want to make sure I'm not reinventing the wheel here. 
Anyone have any idea?
You should use the latest version of bcftools, and you should get exactly what you want.  However you would have to take time to make the `-f` string perfect.  For example:

    bcftools query --print-header -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT\t%RO\t%AO]\n' file.vcf.gz