Variant calling from comparison of assembled genomes where there is only one read depth.
I have generated two sorted bam files using minimap2 with the flag -ax asm5. Each of the files is a comparison of an assembled genome from a specific individual to a reference genome. I used bcftools mpileup and bcftools call to call variants:
bcftools mpileup -Ou -f ref.fasta ind1.bam ind2.bam | bcftools call -Ov -m >var.vcf
In the vcf file I get GT 0/1 0/1 on positions where I see in IGV browser that one of the genotypes have SNP while the other does not. I guess that bcftools pipeline in not designed to call variants with 1 read depth. Is there a way to call variants with 1 read depth using bcftools? Is there a better alternative? I do not have the raw reads from which these individual assemblies were generated.
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