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
freebayes and filtered variants for exonic regions using
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?