How to merge VCF files without duplicates

0

Hey guys,
I want to merge VCF files without containing any duplicates which are generated from three different variant callers. The BAM file is the same for all three variant callers.

1.BCFtools

bcftools mpileup -Ou -f hg19.fa.gz NIST7035_BWA_Samtools_sorted_PCR_RG.bam | bcftools call -mv -Ov -o NIST7035_BWA_Samtools_sorted_PCR_RG_bcftools_call.vcf

2.GATK HaplotypeCaller

java -jar -Xmx6G gatk.jar HaplotypeCaller -R /mnt/x/linux/NIST_Garvan/hg19.fa.gz -I /mnt/x/linux/NIST_Garvan/NIST7035_BWA_Samtools_sorted_PCR_RG.bam -O /mnt/x/linux/NIST_Garvan/NIST7035_BWA_Samtools_sorted_PCR_RG_GATK_HaplotypeCaller.vcf

3.Freebayes**

freebayes -f hg19_freebayes.fa NIST7035_BWA_Samtools_sorted_PCR_RG.bam > NIST7035_BWA_Samtools_sorted_PCR_RG_Freebayes.vcf

I am using bcftools merge, but I think I am getting duplicate calls.

A suggestion with the command line will be very helpful.

Thank you!


vcf

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