I am creating a gene sequence for a sample in the vcf using a standard reference genome. The command for generating the sequence I found on this site works well.
samtools faidx ref.fasta chrom:start-stop | bcftools consensus -s sample my.vcf
But I have separate SNP and INDEL vcf files generated using GATK UnifiedGenotyper. I would like to merge these files so I can generate a consensus sequence from a reference. I want to include the INDELS but I am having trouble finding information on what happens with common tools used to join these vcf files.
Tools like: GATK CombineVariants
Any ideas would be appreciated.