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====1. vt cannot retrieve sequences from my reference sequence file ====
====1. vt cannot retrieve sequences from my reference sequence file ====
It is common to use reference files based on the UCSC browser's database and from the Genome Reference Consortium.
It is common to use reference files based on the UCSC browser's database and from the Genome Reference Consortium.
For example, HG19 vs GrCH37. The key difference is that chromosome 1 is represented as chr1 and 1 respectively in the
For example, HG19 vs GrCH37. The key difference is that chromosome 1 is represented as chr1 and 1 respectively in the
FASTA files from these 2 sources. Just use the appropriate FASTA file that was used to generate your VCF file in originally.
FASTA files from these 2 sources. Just use the appropriate FASTA file that was used to generate your VCF file in originally.
