Distinguish alleles of a SNP in trio VCF files

Question

[charlesberkn]

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.

[charlesberkn]

Thank you all guys, I will try your suggestions.

[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.

[Pierre Lindenbaum]

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

[charlesberkn]

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

Answer 1

[reza.jabal]

Hi,

1. Convert your VCF files to annovar files (see here)
2. Use Microsoft excel VLOOKUP function to match segregation consistent variants.

Answer 2

[cpad0112]

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

Answer 3

[Pierre Lindenbaum]

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

[reza.jabal]

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