I need to add into my VCFs the AF INFO field, which is not output when variant calling with samtools/bcftools.
I think this can be done with the bcftools annotate command and the AF tag is mentioned in the Expressions part of the bcftools man page. (http://www.htslib.org/doc/bcftools.html#ex ...
... I've not used Conifer so I don't know how it identifies and outputs CNVs.
Could it be that the CNV chromosome positions differ slightly between each person in the family? So when you're looking for the inherited region, it's there but just slightly different position callings in each cousin?
I'd m ...
... I'm trying to do some CNV calling from Illumina Omni2.5 array data using penncnv.
My array data is from a few different 'versions' of the Omni2.5 arrays (some from 2011, some from 2013 and some from 2014) so the SNP names have changed between versions as dbSNP is updated. I've tried combining the 2 ...
... HI all,
Thanks for the tips. The solution ended up being 'take the laptop home away from the nasty university proxy and install'. Running smoothly now.
... I have spent some time trying to get MuSiC to work through Ubuntu. The initial installation command:
wget -q -O - https://apt.genome.wustl.edu/ubuntu/files/install.sh | sudo bash
sits for quite some time not achieving anything. So I attempted to follow the repository linking commands but at