Posts: 294
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Can someone tell me the code to make a subset, as I only want certain samples and I can’t merge with the whole dataset
Thanks
Target: Son_scaled
Distance: 0.6744% / 0.00674389
40.0 Turkey_N
24.0 Morocco_Epipaleolithic
16.2 SSA
9.8 Steppe
6.4 Levant_Meoslithic
1.8 AUS_Willandra_Lakes_4000BP
1.0 Iran_N
0.4 CHG
0.4 Ethiopia_Mota_4500BP
Target: Me
Distance: 1.5863% / 0.01586331
30.2 Turkey_N
24.2 Levant_Meoslithic
19.2 Morocco_Epipaleolithic
13.6 SSA
6.0 Steppe
5.6 Iran_N
1.2 CHG
Target: Wife_scaled
Distance: 1.2358% / 0.01235821
38.0 Turkey_N
30.2 Morocco_Epipaleolithic
16.2 SSA
11.8 Steppe
3.8 Levant_Meoslithic
Posts: 517
Threads: 39
Joined: Aug 2023
Gender: Male
Ethnicity: Colonial American
Nationality: American
Y-DNA (P): R1b-U152 >R-FTA96415
Y-DNA (M): I2-P37 > I-BY77146
mtDNA (M): J1b1a1a
mtDNA (P): H66a
--keep samples2keep.txt
Provide it a file with a list of sample IDs to retain.
Genetics189291 likes this post
Posts: 294
Threads: 54
Joined: Nov 2023
Gender: Male
Ethnicity: Arab
(09-20-2024, 01:35 PM)AimSmall Wrote: --keep samples2keep.txt
Provide it a file with a list of sample IDs to retain.
Can you provide me with the rest of the command as well thanks
Target: Son_scaled
Distance: 0.6744% / 0.00674389
40.0 Turkey_N
24.0 Morocco_Epipaleolithic
16.2 SSA
9.8 Steppe
6.4 Levant_Meoslithic
1.8 AUS_Willandra_Lakes_4000BP
1.0 Iran_N
0.4 CHG
0.4 Ethiopia_Mota_4500BP
Target: Me
Distance: 1.5863% / 0.01586331
30.2 Turkey_N
24.2 Levant_Meoslithic
19.2 Morocco_Epipaleolithic
13.6 SSA
6.0 Steppe
5.6 Iran_N
1.2 CHG
Target: Wife_scaled
Distance: 1.2358% / 0.01235821
38.0 Turkey_N
30.2 Morocco_Epipaleolithic
16.2 SSA
11.8 Steppe
3.8 Levant_Meoslithic
Posts: 517
Threads: 39
Joined: Aug 2023
Gender: Male
Ethnicity: Colonial American
Nationality: American
Y-DNA (P): R1b-U152 >R-FTA96415
Y-DNA (M): I2-P37 > I-BY77146
mtDNA (M): J1b1a1a
mtDNA (P): H66a
plink(version number) --bfile "dataset" --keep extractlist --make-bed --out "your sample"
Genetics189291 likes this post
Posts: 294
Threads: 54
Joined: Nov 2023
Gender: Male
Ethnicity: Arab
(09-20-2024, 02:02 PM)AimSmall Wrote: plink(version number) --bfile "dataset" --keep extractlist --make-bed --out "your sample"
Is their a way of doing it for eigenstrat format, because the dataset is in eigrnstrat. Wouldn’t they output it in a different format?
Target: Son_scaled
Distance: 0.6744% / 0.00674389
40.0 Turkey_N
24.0 Morocco_Epipaleolithic
16.2 SSA
9.8 Steppe
6.4 Levant_Meoslithic
1.8 AUS_Willandra_Lakes_4000BP
1.0 Iran_N
0.4 CHG
0.4 Ethiopia_Mota_4500BP
Target: Me
Distance: 1.5863% / 0.01586331
30.2 Turkey_N
24.2 Levant_Meoslithic
19.2 Morocco_Epipaleolithic
13.6 SSA
6.0 Steppe
5.6 Iran_N
1.2 CHG
Target: Wife_scaled
Distance: 1.2358% / 0.01235821
38.0 Turkey_N
30.2 Morocco_Epipaleolithic
16.2 SSA
11.8 Steppe
3.8 Levant_Meoslithic
Posts: 517
Threads: 39
Joined: Aug 2023
Gender: Male
Ethnicity: Colonial American
Nationality: American
Y-DNA (P): R1b-U152 >R-FTA96415
Y-DNA (M): I2-P37 > I-BY77146
mtDNA (M): J1b1a1a
mtDNA (P): H66a
I don't know. I don't deal in eigenstrat, I convert them as the tools I utilize prefer plink format.
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