Similarity between reference files
I have generated a consensus sequence of a bam file using
samtools mpileup -uf /media/shayantanbanerjee/disk21/Ref/hg38.fa stjude.bam | bcftools call -c | vcfutils.pl vcf2fq > cns_stjude.fq
Now I want to find how close this file is to the human reference hg38.fa. How can I do that? I am looking for a tool that outputs some x% similarity between the two files.
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