This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to detect de novo variants with trio-data

Hi, all.

I have a trio-dataset of a kind of fish with whole genome sequence: father, mother and offspring. I want to get information of de novo variant sites from this trio-dataset.

How can I check for variants present in descendants that are not present in either parent, and look for variant sites with Mendelian violations?

I'd appreciate any ideas on creating a methodology to go about this analysis.

wgs trio denovo variants
• 2,336 views • link
written by Shin Taguchi • Shin Taguchi

2 answers

Look for KGGSEQ

• 0 views • link
written by pragnapcu • pragnapcu

gatk: gatk VariantAnnotator -R "ref.fasta" -V fam.vcf -A PossibleDeNovo -O fam.denovo.vcf -ped fam.ped

bcftools https://samtools.github.io/bcftools/howtos/plugin.trio-dnm2.html

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

@Pierre Lindenbaum

Thank you for your comment.

When using GATK, is the file specified in option -V a VCF file with the trio (father, mother, child) merged and variants called?

• 0 views • link
written by Shin Taguchi • Shin Taguchi

Thank you very much!

I'm considering the following pipeline in broad terms. How do you think about this?

Raw data

Adapter trim (Trimmomatic)

Mapping (BWA)

Sorting and removing duplicates (samtools and picard)

Gnenotyping each individual (GATK: HaplotypeCaller)

Merging trio (GATK: CombineGVCFs)

Joint genotyping (GATK: GenotypGVCFs)

Select variants (GATK: SelectVariants)

Hard filtering (GATK: VariantFiltration)

Selecting de novo variants (GATK: VariantAnnotator)

• 0 views • link
written by Shin Taguchi • Shin Taguchi

Log in to answer this question.

More posts like this