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.
Thank you



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