Assuming I have the following two lines in a VCF, both of which code for a pathogenic variation in the MASP1 gene:
chr3 187235874 . C T 338.10 PASS AB=0.611111;ABP=4.9405;AC=2;ADP=16;AF=0.5;AN=4;AO=11;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.20771;EPPR=3.32051;GTI=0;HET=1;HOM=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NC=0;NS=1;NUMALT=1;ODDS=47.5715;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=437;QR=294;RO=7;RPP=4.78696;RPPR=3.32051;RUN=1;SAF=6;SAP=3.20771;SAR=5;SF=0,1;SRF=6;SRP=10.7656;SRR=1;TYPE=snp;WT=0 GT:ABQ:DP:ADR:GQ:ADF:RO:RDF:AD:GL:RDR:QA:RD:SDP:AO:PVAL:QR:RBQ:FREQ 0/1:.:18:.:.:.:7:.:.:-10,0,-10:.:437:.:.:11:.:294
and
chr3 187236382 . G A 351.81 PASS AB=0.611111;ABP=4.9405;AC=2;ADP=15;AF=0.5;AN=4;AO=11;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.20771;EPPR=10.7656;GTI=0;HET=1;HOM=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NC=0;NS=1;NUMALT=1;ODDS=45.4512;PAIRED=0.909091;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=457;QR=294;RO=7;RPP=4.78696;RPPR=10.7656;RUN=1;SAF=8;SAP=7.94546;SAR=3;SF=0,1;SRF=5;SRP=5.80219;SRR=2;TYPE=snp;WT=0 GT:FREQ:QR:RBQ:AO:PVAL:QA:SDP:RD:RDR:GL:ADF:RDF:RO:AD:GQ:ADR:ABQ:DP 0/1:.:294:.:11:.:457:.:.:.:-10,0,-10:.:.:7:.:.:.:.:18
This is bad news if one mutation is located in one allele and the other in the other allele of the patient's chromosome. Is there a way to tell this from a VCF file, or is it necessary at the point of finding multiple occurrences such as these to go back BAM files to figure out whether one copy of a gene is twice damaged or there are two damaged genes?
So, essentially, you want to phase your variants to find which are on the same chromosome?
There are tools for that. Now you know the right terminology and you can try some googling ;-)
But obviously, with short reads you are quite limited. If reads don't span from SNP A to SNP B it gets hard.