I have WGS data for 8 individuals (the same ethnic group, but presumably unrelated) with 30X by illumina . for each individual, they have ~3.6 million called SNPs. When I combine them, there are totally 9.3 million SNPs called in at least one individual... is the number normal or not?
I found several snps whose allele frequencies are very rare in 1000 genome/EXP exome, but the rare homozygous genotypes are shared by several individual in the panel, which really worries me... is it normal or somehow indicative of cross-contamination?
Thank you!
I found several snps whose allele frequencies are very rare in 1000 genome/EXP exome, but the rare homozygous genotypes are shared by several individual in the panel, which really worries me... is it normal or somehow indicative of cross-contamination?
Thank you!