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Distinguish alleles of a SNP in trio VCF files

Hi All,

I have three VCF files, one for father, one for mother, and one for son. I want to distinguish each allele of a SNP in son's VCF file from father or mother, just like a Mendelian analysis of inheritance. Are there any tools or proper way to achieve this? Thanks.

snp
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updated by Ram Ram • written by charlesberkn • charlesberkn

Thank you all guys, I will try your suggestions.

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updated by Ram Ram • written by charlesberkn • charlesberkn

Hi All,

I have tried three ways suggested above, but based on my personal experience, they are not easy to use. I just want to know if there are any other tools available. Thanks.

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updated by Ram Ram • written by charlesberkn • charlesberkn

what would be a tool easy to use for your personal experience ? what's missing in the other tools ?

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written by Pierre Lindenbaum Pierre Lindenbaum

For example, I used CombineVariants to combine vcf files, but it cannot handle different records in the CHROM field as I posted here.

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updated by Ram Ram • written by charlesberkn • charlesberkn

3 answers

Hi,

  1. Convert your VCF files to annovar files (see here)
  2. Use Microsoft excel VLOOKUP function to match segregation consistent variants.
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updated by Ram Ram • written by reza.jabal reza.jabal

If they are in single VCF file, I would have suggested, vcf-contrast or GATK select variant walker.

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updated by Ram Ram • written by cpad0112 cpad0112

Merge with gatk CombineVariants

You might use my tool to find whether the uncalled sites were REF/REF or ./.

Extract the Mendelian incompatibilities with PhaseByTransmission

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Pierre have you got a piece of code that query intersections in ANNOVAR files?

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written by reza.jabal reza.jabal

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