I have cDNA variant of LRG (Refseq) sequences (e.g. NM_020469.2:c.467C>T) want to convert to hg19 genomic co-ordinate. For the same I am using "NCBI Genome Remapping Service- clinical remap " online service.
I have data on : LRG
I want to map to:hg19
Problem is in vcf output when I go to UCSC hg19 same genome position it shows me different basepair(136136770=> A [but the output given by clinical remap is G for same postion]) than clinical remap output .
So from the vcf output, all reference base pairs are not matching with UCSC hg19 genome base pair.
Can anyone please tell me the reason and help to convert my cDNA LRG variant to hg19 genomic coordinate.
Thank you In advance,