Distinguish alleles of a SNP in trio VCF files
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5.6 years ago
charlesberkn ▴ 30

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 • 2.1k views
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Thank you all guys, I will try your suggestions. 

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

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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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5.6 years ago
reza.jabal ▴ 460

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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5.6 years ago

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

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5.6 years ago

merge with gatk CombineVariants https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php

you might use my tool https://github.com/lindenb/jvarkit/wiki/FixVcfMissingGenotypes to find wether the uncalled sites were REF/REF or ./.

extract the mendelian incompatibilities with PhaseByTransmission

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

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