[Vcftools-help] bug in vcftools 0.1.17

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Dear vcftools maintainers,

there seems to be a bug in the recent vcftools version. When using GATK HaplotypeCaller it seems to be possible to get a missing position phased and the GT sub-field will then be ".|.":

                  GT:AD:DP:GQ:PGT:PID:PL:PS       .|.:0,0:.:.:0|1:132964_A_G:.:132964

However, when using vcftools on such an vcf, the field will not be preserved, but recoded to ".", which than causes errors in other programs:
                  GT:AD:DP:GQ:PGT:PID:PL:PS       .:0,0:.:.:0|1:132964_A_G:.:132964

Hope I could help you If you were not aware of this by now.

Regards

Johannes Geibel
_____________________________________
Johannes Geibel
Animal Breeding and Genetics Group
University of Goettingen
Department of Animal Sciences
Center for Integrated Breeding Research (CiBreed)
Albrecht-Thaer-Weg 3, 37075 Goettingen
Tel.: +49-551-3925609, Fax: +49-551-395587
Email: joh...@un...<mailto:joh...@un...>
http://www.uni-goettingen.de/tierzucht