Hapbin Physical Map Info

[paolo002]

Hi, the new hapbin 1.3 version is giving me now 5 columns instead than 2 only which were given by old version: Location iHH_0 iHH_1 iHS std iHS

Since I am providing map file to calculate iHS, is it possible to have in the output an additional 6th column with the info of the location (from physical or genetic map)? Because the column which here is indicated as "Location" gives the info about the SNP name (ID) but not the exact number of the location (locus ID).

Regards

[paolo002]

the same problem occurs when I calculate XPEHH by the way

[camaclean]

Hi,

Yeah, I can add an Index column and perhaps rename to Location to SNP_ID to make the distinction clearer.

-Colin

[paolo002]

Hi Colin

Yes, please, if possible can you do that? Last time you added the two columns iHH_0 iHH_1 and the standardised iHS and the XPEHH columns in the output which were very useful. Thanks a lot. If it is possible to have a column with the SNP ID and then also a column for the correspondent location of the SNP on the genome coming from the input map file given, would be really great. I think in selscan output that information is provided so it would be great to have in hapbin something similar to that. Thanks a lot again! Regards Paolo

[camaclean]

I added the zero-indexed ID. You can then use that to find the corresponding ID in the map file.

[prenderj]

Hi Colin

Do you mean variant position minus one? This may be confusing for users. Actual variant position from the map file would be more useful. Though in the mean time Paolo if in a hurry can just put SNP position in id.

On Monday, 5 November 2018, camaclean notifications@github.com wrote:

I added the zero-indexed ID. You can then use that to find the corresponding ID in the map file.

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[camaclean]

Well, it is the position, just counting starting from zero the way you would in most programming languages. This way you don't have to do any offset when looking up map[index].

[paolo002]

Thank you very much!, having the info about the SNP position in the output is very useful. If you can update again the version 1.3.0 in the conda repository as you guys did last time it would be great.