Hapmap to vcf

Question

[shinken123]

Hi all,

I have a hapmap file from tassel and I want to convert it to a vcf. Tassel can convert the file but takes the major allele as the reference and the minor as the alternative.

I want to use the reference genome for the reference alleles and set the alleles different from the reference genome as the alternative. I also tried GATK but it gives me the error NULL alleles are not supported.

My hapmap file looks like this and is tab deleimited:

rs# alleles chrom   pos strand  assembly#   center  protLSID    assayLSID   panelLSID   QCcode  sample1 sample2 sample3 sample4 sample5 sample6 sample7 
S1_134  C/T 1   134 +   N   N   N   N   N   N   C   C   C   N   N   C   C   
S1_204  G/A 1   204 +   N   N   N   N   N   N   G   G   R   N   N   G   G   
S1_340  C/T 1   340 +   N   N   N   N   N   N   C   C   C   N   N   C   C   
S1_477  C/T 1   477 +   N   N   N   N   N   N   C   C   Y   N   C   C   C   

There is a tool to perform what I want?

Best,
Eric

[finswimmer]

I want to use the reference genome for the reference alleles and set the alleles different from the reference genome as the alternative.

You can correct this using bcftools +fixref:

$ bcftools +fixref input.vcf -Ov -o output.vcf -- -f genome.fa -m flip

fin swimmer