Tool to obtain phased genotypes for family quartet?

Question

[pristanna]

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!

Answer 1

[Vivek]

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

There are other options like deNovoGear, Beagle etc.

Answer 2

[Len Trigg]

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. (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.

[pristanna]

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!