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Polish_genome
Hi, author: I want to polish the assembled genome and then get consensus FASTA, using Merfin. I now have FastA files and Illumina Reads FastQ files; How do I get a VCF file?Is it possible to use GATK to map FASTQ reads to the self-assembled genome FASTA? Look forward to hearing from you, thanks! With best wishes.
Hello @yao-chenxin , sorry for the very delayed reply. Yes, you could use GATK or DeepVariant. Up to you. I assume the assembly wasn't generated from Illumina reads though?
Best, Arang