Question: Tool to obtain phased genotypes for family quartet?
0
gravatar for pristanna
4.2 years ago by
pristanna520
Czech Republic
pristanna520 wrote:

Dear all,

could anyone recommend me a command line tool / strategy to obtain phased genotypes for family quartet from NGS data? The output should be VCFv4.1 (in order to be able to upload it to GEMINI db).

Thanks a lot for your ideas!

 

ADD COMMENTlink modified 4.2 years ago by Len Trigg1.2k • written 4.2 years ago by pristanna520
1
gravatar for Vivek
4.2 years ago by
Vivek2.2k
Denmark
Vivek2.2k wrote:

Fastest and easiest would be GATK's PhaseByTransmission, just supply the VCF and pedigree information.

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_phasing_PhaseByTransmission.php

There are other options like deNovoGear, Beagle etc

http://sourceforge.net/projects/denovogear/

http://faculty.washington.edu/browning/beagle/beagle.html

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Vivek2.2k
1
gravatar for Len Trigg
4.2 years ago by
Len Trigg1.2k
New Zealand
Len Trigg1.2k wrote:

You don't say much about where your starting point is, I assume it is right from NGS reads. One streamlined approach you can use is Real Time Genomics software for both mapping and variant calling: http://realtimegenomics.com/products/rtg-core/ (It is free for non-commercial use). In particular, the RTG variant caller directly incorporates the pedigree information (both relationships and sex) for your quartet during the variant calling, and outputs phasing information where this can be derived according to the pedigree.

 

 

ADD COMMENTlink written 4.2 years ago by Len Trigg1.2k

I have fastq files, bam files, vcf files - so I can start from whatever point. RTG looks promising, it should be able to analyze also the quartet. Because GATK and Beagle as far as I know could analyze just trios. So thanks a lot for your recommendation!
 

ADD REPLYlink written 4.2 years ago by pristanna520
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