I have multiple single-sample VCF files, which I want to merge into a single multi-sample VCF file. When using `bcftools merge` I am getting duplicate records. 

    $ bcftools merge ms01e_phased.vcf.gz ms02g_phased.vcf.gz ms03g_phased.vcf.gz ms04h_phased.vcf.gz MA605_phased.vcf.gz MA611_phased.vcf.gz -O v -o RBphased_variants.SixSamples.Final.vcf
     # duplicate records at the same lines from the file "RBphased_variants.SixSamples.Final.vcf"
    2	14691373	.	A	.	1153.31	PASS	BaseQRankSum=2.02;ClippingRankSum=0;ExcessHet=3.0103;FS=1.098;InbreedingCoeff=-0.0861;MQ=58.74;MQRankSum=-2.459;QD=19.22;ReadPosRankSum=-0.466;SOR=0.96;DP=68;AN=8	GT:AD:DP:GQ:PL:PG:PB:PI:PW:PC:PM	0/0:4:4:0:0:0/0:.:.:0/0:.:.	0/0:7:7:18:0:0/0:.:.:0/0:.:.	0/0:4:4:12:0:0/0:.:.:0/0:.:.	0/0:2:2:3:0:0/0:.:.:0/0:.:.	./.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.
    2	14691373	.	A	AAG	1153.31	PASS	BaseQRankSum=2.02;ClippingRankSum=0;ExcessHet=3.0103;FS=1.098;InbreedingCoeff=-0.0861;MQ=58.74;MQRankSum=-2.459;QD=19.22;ReadPosRankSum=-0.466;SOR=0.96;set=InDels;DP=676;AF=0.042;AN=4;AC=0	GT:AD:DP:GQ:PGT:PID:PL:PG:PB:PI:PW:PC:PM	./.:.:.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.:.:.	0/0:12,0:12:9:.:.:0,9,135:0/0:.:.:0/0:.:.	0/0:22,0:22:12:.:.:0,12,180:0/0:.:.:0/0:.:.
    2	14691374	.	A	.	1320.25	PASS	BaseQRankSum=-1.049;ClippingRankSum=0;ExcessHet=0.2929;FS=0;InbreedingCoeff=0.4006;MQ=55.35;MQRankSum=0;QD=33.01;ReadPosRankSum=-0.671;SOR=0.892;DP=44;AN=2	GT:AD:DP:GQ:PL:PG:PB:PI:PW:PC:PM	0/0:4:4:0:0:0/0:.:.:0/0:.:.	./.:7:7:.:0:./.:.:.:./.:.:.	./.:0:0:.:0:./.:.:.:./.:.:.	./.:0:0:.:0:./.:.:.:./.:.:.	./.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.
    2	14691374	.	A	G	1320.25	PASS	BaseQRankSum=-1.049;ClippingRankSum=0;ExcessHet=0.2929;FS=0;InbreedingCoeff=0.4006;MQ=55.35;MQRankSum=0;QD=33.01;ReadPosRankSum=-0.671;SOR=0.892;set=HignConfSNPs;DP=710;AF=0.115;MLEAC=3;MLEAF=0.115;AN=4;AC=0	GT:AD:DP:GQ:PGT:PID:PL:PG:PB:PI:PW:PC:PM	./.:.:.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.:.:.	./.:.:.:.:.:.:.:.:.:.:.:.:.	0/0:12,0:12:9:.:.:0,9,135:0/0:.:.:0/0:.:.	0/0:22,0:22:12:.:.:0,12,180:0/0:.:.:0/0:.:.

I raised this issue in `bcftools` thinking if it was a bug https://github.com/samtools/bcftools/issues/754 . But, is there any other solution to the problem.



Hey kirannbishwa01,

I would not call these duplicate records as they are different calls but at the same position.

Just adding `--merge all` to your command should help to solve it

So:

    bcftools merge --merge all ms01e_phased.vcf.gz ms02g_phased.vcf.gz ms03g_phased.vcf.gz ms04h_phased.vcf.gz MA605_phased.vcf.gz MA611_phased.vcf.gz -O v > RBphased_variants.SixSamples.Final.vcf

Kevin
