Ambiguous position in SNPdb file and reference genome

Question

[misterie]

Hi,

I have problem with ambiguous base in SNPdb (BQSR) file and reference genome. The first 2 line of SNPdb (BQSR) looks like:

CHROM   POS ID  REF ALT QUAL    FILTER  INFO

1   162362  rs477108567 G   A   .   .   .

so that seems in position 162362 in 1 chromosome in my reference genome I should expect G, but there is A. What is a problem. Those 2 files represent the same reference. Any ideas?

Thank you in advance.

[Pierre Lindenbaum]

which build ? which "SNPdb" ?

[misterie]

SNPdb file is ARS1.2PlusY_BQSR.vcf.gz, reference genome is ARS-UCD1.2_Btau5.0.1Y.fa

Answer 1

[Pierre Lindenbaum]

REF Base chr1:162362 is a 'G'

$ curl -s -L "https://sites.ualberta.ca/~stothard/1000_bull_genomes/ARS-UCD1.2_Btau5.0.1Y.fa.gz"  |\
  gunzip  -c | grep -v '>' | fold -w 1 | nl | grep -m 1 -w 162362

 162362 G

REF base in VCF is G and alternate base is A.

I don't see any problem.