I keep ran into trouble while trying to normalize a clinvar VCF file with vt program, hg19 build. Tried every latest hg19/v37 reference fasta but still having the same error:
[variant_manip.cpp:96 is_not_ref_consistent] reference bases not consistent: Y:555381-555381 A(REF) vs N(FASTA) [normalize.cpp:209 normalize] Normalization not performed due to inconsistent reference sequences. (use -n or -m option to relax this)
Do you know anywhere to find the reference file clinvar used to build their latest GRCh37 VCF, or anyway to solve this problem? Much appreciated!