Jovialis
Advisor
- Messages
- 9,313
- Reaction score
- 5,878
- Points
- 113
- Ethnic group
- Italian
- Y-DNA haplogroup
- R-PF7566 (R-Y227216)
- mtDNA haplogroup
- H6a1b7
This is how I did it,
I aligned the FASTQ to HG19 with BWA Creating the SAM file
Then I created the BAM file which I then sorted, indexed, and marked for duplicates
I then used WGSextract to create the BAI and 23andme_V3.txt file.
I then used Plink 1.9 to convert it to a VCF.
From the VCF I create the Plink files.
Finally, I converted it with Eigensoft to Eigenstrat, and merged with the Reich Lab data base.
I will finally proceed with my downstream analysis in Admixtools.
I aligned the FASTQ to HG19 with BWA Creating the SAM file
Then I created the BAM file which I then sorted, indexed, and marked for duplicates
I then used WGSextract to create the BAI and 23andme_V3.txt file.
I then used Plink 1.9 to convert it to a VCF.
From the VCF I create the Plink files.
Finally, I converted it with Eigensoft to Eigenstrat, and merged with the Reich Lab data base.
I will finally proceed with my downstream analysis in Admixtools.