Hi Alex, With regards to the haplotype sorting window, each genotype's haplotypes are sorted and displayed independently, so they truly are haplotypes. The two haplotypes of a heterozygous genotype will end up in different clusters which means that it isn't possible to use the term "heterozygous haplotype". There isn't an indication of which chromosomes/haplotypes are paired with which.
Also, the display is best used when genotypes are phased because it often doesn't have enough info to do a sensible clustering. For the genotype data, it appears that you have uncovered a bug. Would it be possible for you to share the header and one or two lines? This would help us in determine the issue and come up with a fix. If you have further questions, please email the list: [email protected]. Thanks! Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Alex Shaw <[email protected]> Date: Mon, Jan 2, 2012 at 5:16 PM Subject: [Genome] Missing data missing from vcf tracks? To: [email protected] Hi there, I've been using the excellent vcf custom track tool. I've noticed that the haplotype sorting window now displays heterogygous genotypes in a different colour, which I like, but seems incorrect to call it a haplotype Also, I'm wondering why missing genotype data is no longer showing up as missing (./.) in the detailed genotypes view, but rather is being switched to homozygous reference. Is this a temporary thing? Thanks, Alex -- Alex Shaw Research Officer Neuroscience Research Australia Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au <http://neura.edu.au/> Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia *T* +61 2 9399 1112 *F* +61 2 9399 1005 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
