Ok. Here is what I have so far. To merge file and included Abusir or any other data file then run through ADMIXTURE or other software
1. Create a .bed, .bim and .fam files for the Abusir from the BAM or FASTQ files
2. Create/download a .bed, .bim and .fam set of files for HGDPor SGDP or whatever population you want to compare with. You can extract a subset of HGDP etc to create a smaller population to compare the Abusir to
3. Merge Abusir with this subset. Eg $ plink --bfile XXXXMAIN_FILE --merge-list all_my_files.txt --make-bed --out XXXXFirst_Merged_File
4. XXXXMAIN_FILE=HGDP subset, all_my_files.txt= text file with files you want to merge.
all_my_files.txt=
[myfileX.bed myfileX.bim myfileX.fam
myfile11.bed myfile11.bim myfile11.fam] ensure one line per sample set. I took me awhile to figure that out. Instructions was not clear.
5. Run through ADMIXTURE and create the *.P and *.Q file. Now you have included the Abusir with your dataset.
6. Barplot in R software
Couple of things to look out for. I got an error….
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@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
|
pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@
Web-based version check ( --noweb to skip )
Recent cached web-check found...Problem connecting to web
Writing this text to log file [ First_Merged_File_BBB.log ]
Analysis started: Wed Dec 05 14:44:45 2018
Options in effect:
--bfile gplink-test-1
--merge-list all_my_files.txt
--make-bed
--out First_Merged_File_BBB
Reading map (extended format) from [ gplink-test-1.bim ]
135056 markers to be included from [ gplink-test-1.bim ]
Reading pedigree information from [ gplink-test-1.fam ]
4899 individuals read from [ gplink-test-1.fam ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 4899 missing
1737 males, 654 females, and 2508 of unspecified sex
Warning, found 2508 individuals with ambiguous sex codes
Writing list of these individuals to [ First_Merged_File_BBB.nosex ]
Reading genotype bitfile from [ gplink-test-1.bed ]
Detected that binary PED file is v1.00 SNP-major mode
Using merge mode 1 : consensus call (default)
Found 7594 SNPs that do not match in terms of allele codes
Might include strand flips, although flipped A/T and C/G SNPs will be undetected)
Writing problem SNPs to [ First_Merged_File_BBB.missnp ]
ERROR: Stopping due to mis-matching SNPs -- check +/- strand?*****