Question: Distinguish alleles of a SNP in trio VCF files
1
gravatar for charlesberkn
5.1 years ago by
charlesberkn20
United States
charlesberkn20 wrote:

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 • 1.9k views
ADD COMMENTlink modified 8 hours ago by Biostar ♦♦ 20 • written 5.1 years ago by charlesberkn20

Thank you all guys, I will try your suggestions. 

ADD REPLYlink written 5.1 years ago by charlesberkn20

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.

ADD REPLYlink modified 12 months ago by RamRS30k • written 5.1 years ago by charlesberkn20

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

ADD REPLYlink written 5.1 years ago by Pierre Lindenbaum131k

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

ADD REPLYlink modified 12 months ago by RamRS30k • written 5.1 years ago by charlesberkn20
0
gravatar for reza.jabal
5.1 years ago by
reza.jabal440
New York, USA
reza.jabal440 wrote:

Hi,

1) Convert your VCF files to annovar files (see here)

2) Use Microsoft excel VLOOKUP function to match segregation consistent variants.

ADD COMMENTlink written 5.1 years ago by reza.jabal440
0
gravatar for cpad0112
5.1 years ago by
cpad011214k
Hyderabad India
cpad011214k wrote:

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

ADD COMMENTlink written 5.1 years ago by cpad011214k
0
gravatar for Pierre Lindenbaum
5.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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

ADD COMMENTlink written 5.1 years ago by Pierre Lindenbaum131k

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

ADD REPLYlink written 5.1 years ago by reza.jabal440
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