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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Amazon bucket for reference files not available #139

Closed jatintalwar closed 4 years ago

jatintalwar commented 4 years ago

Hello,

I am trying to use the canvas variant caller for WGS workflow but i am unable to download the required reference files from Amazon bucket as it seems to be not available.
http://canvas-cnv-public.s3.amazonaws.com/

Could you please take a look?

In addition, i have question regarding the reference files: I have a reference fasta file and want to create my own files that i can use for running Canvas. For example i created a GenomeSize.xml file which looks like this:

chr1    248956422
chr10   133797422
chr11   135086622
chr12   133275309
chr13   114364328
chr14   107043718

I am wondering if this work? if not, can you please share some information on how to generate a GenomeSize.xml that can be used for the specific genome.fa that we might have?

Thank you very much!

eroller commented 4 years ago

it still works for me.

try this: wget http://canvas-cnv-public.s3.amazonaws.com/hg19/WholeGenomeFasta/GenomeSize.xml

Look at that file for the correct format for GenomeSize.xml

jatintalwar commented 4 years ago

Thanks @eroller

Worked for me with http(s). Something with the security profile for us internally was the issue. But thanks for the information on the xml file. I will modify the xml according to genome of interest for me.