An Indian population specific polymorphic Alu insertion map
Here, we report the genomic landscape of Alu InDels from the recently released 1,021 Indian Genomes (IndiGen). Annotations for the QC filtered Alus are available at https://clingen.igib.res.in/indigen. We identified 9,239 polymorphic Alu insertions that include private (3,831), rare (3,974), and common (1,434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified indels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; amongst these, 58% (1,289 sites) were common polymorphisms in IndiGen.
The vcf calls for the Alus passing genotype missingness criterion are provided. The raw bam file data will be provided upon request, access to which could be requested by mail to Dr. Jyoti Yadav ([email protected]), the convener of the Institutional Human Ethics Committee of CSIR-IGIB.
The tools and softwares that were required to process the data:
- VCFTOOLS
- PLINK
- bedtools
- bedops
- R