variant calling using masked reference genome
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7 months ago
reza ▴ 270

hi

I want to start a variant calling process using reference genome. Since most reference genomes in NCBI are masked (Some parts of the genome are marked with small letters), do I need to convert lowercase to uppercase before starting the process?

Will the manipulation or non-manipulation of the reference genome affect the final results?

Thanks

Bowtie2 Reference Genome Variant Calling • 198 views
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