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316 bytes added, 21:35, 21 September 2015
1. vt cannot retrieve sequences from my reference sequence file
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 originally.
Another common issue is due to the corruption with the indexed file of the reference sequence, say for a reference file named
hs37d5.fa or hs37d5.fa.gz, simply delete the index file denoted by hs37d5.fa.fai or hs37d5.fa.gz.fai and run the vt command
again. A new index file will be generated automatically.
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