Discordance genotyping

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PierreJus

• March 28, 2022 20:31

Hi All,

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.

Pierre

 

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  Genevieve Brandt (she/her)

  • April 06, 2022 22:43

  Hi PierreJus,

  We have a couple troubleshooting articles that might help you get started in determining why GATK did or did not call certain variants:

  • Expected variant at a specific site was not called
  • When HaplotypeCaller and Mutect2 do not call an expected variant

  Take a look and let us know if you have any other questions.

  Best,

  Genevieve

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