QTNs with unknown name and position

ddenne...@uni-kassel.de

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Oct 5, 2018, 6:34:00 AM10/5/18

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Dear BLINK team,

thank you for your hard work. I'm testing your last version of BLINK-C (2018-10-) for mac within GAPIT 3.0 (2018-08-18). However I noticed that the output generated by the GAPIT 3.0 script containing quite a number of QTNs with unknown name and position. I was wondering is this intentionally or went something wrong?

I couldn't find an example output of BLINK, which would confirm or don't confirm that output.

Could you please explain me this results? It would be very helpful indeed.

Kind regards,
Dominic

Example:

SNP Chromosome Position P.value effec maf nobs
1 .4 0 0 3.203835e-08 NA 0.45151520 165
2 .424 0 0 3.577661e-08 NA 0.07272727 165
3 Excalibur_c18410_136 10 79 4.750984e-07 NA 0.42424240 165
4 .5906 0 0 1.653237e-06 NA 0.41212120 165
5 .9293 0 0 2.752070e-06 NA 0.21818180 165
6 .2 0 0 5.924678e-06 NA 0.07575758 165
7 GENE-3626_308 13 42 1.591204e-05 NA 0.07878788 165
8 Excalibur_c41477_1272 9 51 1.820812e-05 NA 0.28181820 165
9 .1 0 0 8.418093e-05 NA 0.12121210 165
10 .4 0 0 3.044981e-04 NA 0.16666670 165

Huang, Meng

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Oct 8, 2018, 10:17:49 AM10/8/18

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Hi Dominic,

I guess your map file include float number (which is indicated as genetical map but not physical map). Actually, the oder of SNP, in the GWAS results, is same as input file, but the name of SNPs are massed up.

I will fix this problem, but please just ignore the wrong name in GWAS results when you use current version.

Thanks,

Meng

------------
Meng Huang, Ph.D.
Postdoc Research Assistant
LSPS 202 Lilly Hall, Department of Agronomy
Purdue University
West Lafayette, IN, 47907

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------------
Meng Huang, Ph.D.
Postdoc Research Assistant
LSPS 202 Lily Hall, Department of Agronomy
Purdue University
West Lafayette, IN, 47907

ddenne...@uni-kassel.de

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Oct 9, 2018, 1:02:06 PM10/9/18

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Hi Meng,

thanks for your quick replay! This hint is very helpful!

Regards,

Dominic

On Monday, 8 October 2018 16:17:49 UTC+2, Huang, Meng wrote:

Hi Dominic,

I guess your map file include float number (which is indicated as genetical map but not physical map). Actually, the oder of SNP, in the GWAS results, is same as input file, but the name of SNPs are massed up.

I will fix this problem, but please just ignore the wrong name in GWAS results when you use current version.

Thanks,

Meng

------------
Meng Huang, Ph.D.
Postdoc Research Assistant
LSPS 202 Lilly Hall, Department of Agronomy
Purdue University
West Lafayette, IN, 47907

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