Does anyone have suggestions for generating the union of alleles file that is fed into glia to perform realignment for freebayes.
I am trying to build a ensemble variant detection pipeline.
I already have two VCFs containing SNPs genotypes discovered in my population.
Eventually i would also like to include SV's from delly.
Can one do a very simple union with bcftools?
Are genotypes needed in the union of alleles file ?
Could dbSNP be used?
Any thoughts appreciated.
I am trying to build a ensemble variant detection pipeline.
I already have two VCFs containing SNPs genotypes discovered in my population.
Eventually i would also like to include SV's from delly.
Can one do a very simple union with bcftools?
Are genotypes needed in the union of alleles file ?
Could dbSNP be used?
Any thoughts appreciated.