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To complete our example analysis, we could run:
TrioCaller --shotgun result/chr20.mpileup.vcf --pedfile ped/triocaller.ped --rounds 20 --prefix result/chr20.triocaller
The format of output file is same as the input file. Here, you might replace chr20.mpileup.vcf with other vcf file (e.g. chr20.polymutter.vcf). <br />
The format of output file is same as the input file. Again, you can review the contents of the updated VCF file using the more command:
Again, you can review the contents of the updated VCF file using the more command:
more result/chr20.triocaller.vcf
more result/chr20.triocaller.vcf
All right. Congratulations! You have come to the end and learned basic skills for the variant calling in trios.
If you have any question, feel free to contact Wei Chen at [mailto:weichen.mich@gmail.com weichen.mich@gmail.com] or Goncalo Abecasis at [mailto:goncalo@umich.edu goncalo@umich.edu]
If you have any question, feel free to contact Wei Chen at [mailto:weichen.mich@gmail.com weichen.mich@gmail.com] or Goncalo Abecasis at [mailto:goncalo@umich.edu goncalo@umich.edu]
