Last update: 20241220

Design PCA SNV INDEL v1

We prepare two datasets:

(a) 1KG reference population: input ${THOUSAND_GENOMES}/phase3.chr"${INDEX}".GRCh38.GT.crossmap.vcf.gz
(b) SwissPedHealth: input ${PRE_ANNOTATION_DIR}/chr${INDEX}_bcftools_gatk_norm.bcf
We prepare with bcftools and convert to bcf.
We then convert to PLINK format.
Prune variants :
- --maf 0.10, only retain SNPs with MAF greater than 10%
- --indep [window size] [step size/variant count)] [Variance inflation factor (VIF) threshold]
- e.g. indep 50 5 1.5, Generates a list of markers in approx. linkage equilibrium - takes 50 SNPs at a time and then shifts by 5 for the window. VIF (1/(1-r^2)) is the cut-off for linkage disequilibrium
Merge to single files
Merge (a) and (b) = (c)
PCA on each of (a-c) for individual datasets and plots

Output: ${PCA_DATA}/prune/

Additional pruning for consideration