Shapeit2 - malformed hap file output?

Question

[mstagliamonte]

Hi,

I have run Shapeit2 using a vcf and a genetic_map file (3 columns) as input. When I look at the hap output file I see the following:

1 A 30016 . G 0 0

According to the documentation, the columns should be so ordered:

1) Chromosome number [integer]

2) SNP ID [string]

3) SNP Position [integer]

4) First allele [string]

5) Second allele [string]

In my output, the 1st column is the chromosome, but I see the alleles on the 2nd and 5th columns. The SNP position (30016) is on column3, and the '.' on 4th column I guess is the SNP ID. Has anyone experienced such an issue?

Thank you for your kind attention,

Max

Answer 1

[mstagliamonte]

OK, Nevermind,

My vcf columns were in the wrong order, from some SNP filtering I had previously done.

Regards,

Max