I´m working with a list of consensus sequences in order to detect variants. I´ve map the consensus to the references senquence using Needleall or BWA-MEM and calling variants with freebayes (v0.9.21). When I check SAM file I can detect indels, but in the vcf generated by freebayes, only SNPs are reported.
Example: AACACACAACAAGAA 0 HXB2_reference 1 255 2D211M1D2M4D9M3I3M2I240M
Could you help me, please?