Question: Merge Samtools and Freebayes vcf files
gravatar for kspata
10 months ago by
kspata60 wrote:


I am analyzing presence of variants in exonic regions of 10 genes. I have sequencing data for samples obtained from different individuals. I aligned the NextSeq PE 150 sequencing data to hg38 human genome assembly using bowtie2 and called variants using samtools and freebayes and filtered variants for exonic regions using bedtools intersect.

I observed some common variants between samtools and freebayes vcf and unique variants in both files. I visualized these variants from both files using IGV which confirms their presence.

Can I merge these two variant files obtained from different tools? If so how can I merge the vcf file?

variants alignment exome • 550 views
ADD COMMENTlink modified 10 months ago by Pierre Lindenbaum123k • written 10 months ago by kspata60
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

gatk CombineVariants with the option genotypemergeoption

    Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
    Take genotypes in priority order (see the priority argument).
    Take the genotypes in any order.
    Require that all samples/genotypes be unique between all inputs.
ADD COMMENTlink written 10 months ago by Pierre Lindenbaum123k
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