Alphagenomics_WheatGBS

Abdullah's Ph.D. project

Genotyping data was geenrated for 51 wheat varieties trough GBS technique.

A: Varitant Calling on GBS data

1. Vairant calling (the variant calling was done by Novogene)
2. Raw VCF files uploaded
3. Variant calling pipeline annd QC
4. Comparison of variant calling with outputs from Novogene
5. Filtered calls

B: SNP analysis across genome

1. Determine the heterozygosity of each SNPs
2. Find minor allele frequency of each SNP and then select those SNPs which having minor allele frequency up to 1 or 2
3. Find the PIC value of each SNPs
4. Analysis of intra and inter genomes/chromosomes variation
5. Calculation of average marker interval
6. Relationship between number of SNPs per chromosome and chromosome physical estimate
7. Correlation of average marker intervals (cM) per chromosomes with physical estimated size of chromosomes.