Hello all,
I’m trying to merge two VCF files.
file1 has an example sequence
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
chr2 29415792 . G A 1101.66 . AB=0.494737;ABP=3.03316;AC=1;AF=0.5;AN=2;AO=47;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=27.4509;EPPR=33.5919;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=231.64;PAIRED=0.978723;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=1807;QR=1719;RO=48;RPL=12;RPP=27.4509;RPPR=33.5919;RPR=35;RUN=1;SAF=47;SAP=105.07;SAR=0;SRF=48;SRP=107.241;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:95:95,47:48:1719:47:1807:-134.266,0,-126.33
file2 has an example sequence
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
chr2 29415792 . G A . PASS ADP=89;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:163:93:89:45:44:49.44%:4.4109E-17:37:18:45:0:44:0
I ran vcf tool to merge the above files and it resulted in the below:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown Sample1
chr2 29415792 . G A 1101.66 PASS AB=0.494737;ABP=3.03316;AC=2;ADP=89;AF=0.5;AN=4;AO=47;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=27.4509;EPPR=33.5919;GTI=0;HET=1;HOM=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NC=0;NS=1;NUMALT=1;ODDS=231.64;PAIRED=0.978723;PAIREDR=0.979167;PAO=0;PQA=0;PQR=0;PRO=0;QA=1807;QR=1719;RO=48;RPL=12;RPP=27.4509;RPPR=33.5919;RPR=35;RUN=1;SAF=47;SAP=105.07;SAR=0;SF=0,1;SRF=48;SRP=107.241;SRR=0;TYPE=snp;WT=0 GT:GQ:ABQ:RDR:RBQ:QR:ADR:FREQ:SDP:DP:AO:RD:GL:ADF:PVAL:RDF:AD:RO:QA:DPR 0/1:.:.:.:.:1719:.:.:.:95:47:.:-134.266,0,-126.33:.:.:.:.:48:1807:95 0/1:163:18:0:37:.:0:49.44%:93:89:.:45:.:44:4.4109E-17:45:44
I understood on how the merging has happened, for the #CHROM, POD, ID, REF, ALT, QUAL, FILTER, INFO fields. However, I couldn’t understand the reasoning on how the FORMAT field is merged.
If someone can explain it or provide some reference links, it will be of great help
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