Question: Tools to check consistency between VCF genotypes and pedigree-stated sex and family relationships
1
gravatar for gaelgarcia
2.5 years ago by
gaelgarcia190
UK
gaelgarcia190 wrote:

We're currently trying to do identity checks on targeted genome sequencing data from ~15K samples. Our target panel is very specific, and only a very small fraction of the sites interrogated by Peddy are covered.

Is there a similar tool you can recommend to verify that the stated stated sex and family relationships match the relationships (relatedness, kinship, etc.) and sex inferred from a VCF?

Related:

Checking kinship coefficients and relationships and comparing genotyping data to exomes

Checking kinship coefficients and relationships and comparing genotyping data to exomes

Question: Obtaining list of / manually specifying interrogation sites in Peddy

Obtaining list of / manually specifying interrogation sites in Peddy

king snp plink gatk vcf • 1.2k views
ADD COMMENTlink modified 2.5 years ago by chrchang5237.3k • written 2.5 years ago by gaelgarcia190

Tagging brentp

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k
1
gravatar for chrchang523
2.5 years ago by
chrchang5237.3k
United States
chrchang5237.3k wrote:

Check for Mendel errors, and be suspicious of any sample with a large number of them. “plink —mendel” is one way to do this.

ADD COMMENTlink written 2.5 years ago by chrchang5237.3k
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