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Fri, 10/31/2014 - 21:10

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jmsoftgenetics's picture
jmsoftgenetics in replay to: First data from GIAB PGP Trios on FTP

I think the VCF file for the latest NA12878 data (3rd link) has an error:

##INFO=<ID=isPolymorphic,Number=1,Type=Flag,Description="Sites that are polymorphic in the CEPH1493 pedigree.">

According to VCF specifications: "The ‘Flag’ type indicates that the INFO field does not contain a Value entry, and hence the Number should be 0 in this case." I don't know how strictly this is usually enforced though.

Related: I tried to use the "Contact GIAB" page instead but it shows an error.

tony wify's picture
tony wify in replay to: Post-ASHG Update on Genome in a Bottle

A very good article on the PGP issue and I've done an extensive research to withhold the truth about the subject. Thanks for the share.
Regards,
Lucas Duplan Clinkle

vasya's picture
vasya in replay to: New high-confidence NA12878 genotypes integrating phased pedigree calls

Yes -- the readme file is not in a plain text format!

SteveL's picture
SteveL in replay to: New high-confidence NA12878 genotypes integrating phased pedigree calls

Thanks for this great resources. I don't know if you have any control over the NCBI ftp site, but the README.GIAB.v0.2.txt file appears to be garbled in some way. Best, Steve