Reference file name from VCF file

Question

[win]

Hi all, is it possible to determine the name of the reference file used from any VCF file?

Thanks in advance.

Answer 1

[Pierre Lindenbaum]

yes if there are some contigs lines in the VCF header.

##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>

yes if there is a reference line in the header:

##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta

yes if you can get a rs# in the ID column with a column CHROM and POS, without any ambiguity

yes if you can check CHROM and POS vs a reference, without any ambiguity