I'm possibly doing something wrong but having problems converting from hg19 to hg38, where my reference call is changed (which changes the user call). I tracked down one example that is reproducible:
#CHROM POS RSID REF ALT QUAL ALLELES
8 129076572 rs13255292 C T . 0/1
(this is hg19 - in this case the user is C/T)
I use crossmap to convert to hg38:
CrossMap.py vcf hg19ToHg38.over.chain.gz test.vcf hg38.fa test-converted.vcf
I am given this output
#CHROM POS RSID REF ALT QUAL ALLELES
8 128064326 rs13255292 A T . 0/1
Reading as it this gives me a A/T for the user.
What am I doing wrong here?
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Hello,
it looks like you have a off-by-one problem in your vcf file. The position for rs13255292 should be 8:129076573 in hg19 and 8:128064327 in hg38.
How do you generate the vcf file?
fin swimmer