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(Quote) And I assume, without coordinates data, I can not do local realignment (or any procedures which involves coordinates) using files in the bundle.
Thank you the reply. It is quite helpful.
Hi. I generated a fasta file (sequences of a gene) and followed what you say. Finally, I did get the whole pineline through (get the vcf file). However, I lost coordinates. This is the fasta format >1 dna:chromosome chromosome:GRCh37:1:19662100…