For a set of samples, I have their genotype from chip-Seq. For the same samples, I also have their raw fastq from NGS sequencing. After calling their SNPs following GATK best practises (1000 genomes), I got a set of SNPs for which the genotype is different for chip-Seq vs. NGS (for example, some are homozygotes with Chip-Seq while the same SNPs are heterozygotes from NGS data).
I want to understand why there are different genotypes between chip-seq and NGS. However, I don't know where I can start to look for an explanation.
Many thanks for any suggestions.
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