I have been trying to create a same-length consensus fasta by mapping reads to a reference genome for input into angsd as the ancestral sequence. However, the scaffolds of the resulting consensus always seem to be a little short, likely due to indels etc.. I have iterated through several versions of code (bcftools call -c or bcftools call -m, not using any data filters, etc.). Is there a specific path or set of filters I should use to be doing this? I found some former issues documented of this in previous versions of samtools/bcftools that had to do with an older version of the program but that doesn't seem to be the issue here. I also tried to use LAST for mapping, but that didn't seem to sort it out.
Apologies for the juvenile question and thanks for any help.