I have a genomic sequence of an inbred mouse strain i.e. the genome is homozygous for a given position or same alleles are present on both of the strands. Now for variant calling, I have to compare it with reference genome and only select homozygous SNPs and Indels (SNPs and Indels that are present on both the strands). If I use this criteria i.e. SNPs and Indels to be present on both the strands, then I am afraid that i might loose some real SNPs and indels because of low coverage (unequal representation of both the strands in the sequencing data) of my data. On the other hand using only one strand may call lot of false positive variants because of sequencing error.
Is there any variant caller designed for homozygous diploid genome that identifies homozygous SNPs and Indels.
I have option of using Freebayes, GATK or Samtools. Which one would be better to use in my case?