Attention:
The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

non-human aneuploid VQSR

CarolineCaroline Hinxton, UKMember
edited October 2013 in Ask the GATK team

Hi all,

I am doing variant calling on each chromosome of each of my samples individually, because each sample can have a different ploidy, which also varies between chromosomes.

I am now looking at the VQSR documentation, and I have discovered that I am on my own! One question people might be able to answer though - if I do the variant calling separately, should I do the VQSR separately as well, or can I combine my variants? I am working on a very short genome and I am not expecting a high density of variants...

Thanks,
Caroline

Best Answer

Answers

Sign In or Register to comment.