LD_pruning error about staarpipeline-tutorial HOT 4 CLOSED

Could you please check the input of the known variant list? How many known variants are in chromosome 1?

from staarpipeline-tutorial.

Could you please check the input of the known variant list? How many known variants are in chromosome 1?

Hi zilin,
Thanks for your reply!

1. I first obtained the rs of the significant genome-wide association variants from GWAS catalog, and approximately 100 variants were genome-wide significant.
2. I then used STAARpipelineSummary_Known_Loci_Info.r to extract the information of CHR, POS, REF and ALT from #rs, but most of the variation information was not extracted, only eight of the variation information was extracted. Here is the information of the known variant list that extracted by STAARpipelineSummary_Known_Loci_Info.r:

CHR       POS REF ALT
1   1 155235843   T   C
2   3 161359842   A   G
3   4    958159   T   C
4   7  23260430   A   C
5  12  40542837   C   T
6  16  28933075   C   G
7  16  30966478   G   A
8  19   2341049   C   T

I checked my individual analysis results generated by STAARpipelineSummary_Individual_Analysis.r, it seems that whenever the sum of variants within a chromosome >1 will arise this error:

Individual analysis results:

"","CHR","POS","REF","ALT","ALT_AF","MAF","N","pvalue",
"","1","24419427","G","A",.......
"","7","","","".......
"","16","","","".......
"","19","",""........

so, chr7,chr16,chr19 have the same error as chr1, here is an example of chr7:

         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 283149 15.2     664202 35.5   450931 24.1
Vcells 486990  3.8    8388608 64.0  1815700 13.9
[1] 7
# of selected samples: 378,834
# of selected variants: 2
# of selected samples: 378,834
# of selected variants: 2
# of selected samples: 380,943
# of selected variants: 992,436
# of selected samples: 378,834
# of selected variants: 0

Then what could be the possible reason for the error? Looking forward to your reply!

Regards,
Yujian

from staarpipeline-tutorial.

Hi Yujian,

Thank you for following up. Have you resolved this issue already? If not, please send an email, and we can discuss it offline.

Best,
Xihao

from staarpipeline-tutorial.

Hi Yujian,

Have you resolved this issue already? I will close this case for now, but feel free to reopen it if you have any questions related to this, or we can discuss it offline.

Best,
Xihao

from staarpipeline-tutorial.