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Created 2014-03-18 21:56:05 | Updated 2014-03-18 21:57:27 | Tags: list combinegvcfs

Comments (5)

it happens with CombineGVCFs, I didn't check other functions.

Running in the current dir /site/ne/data/ngs/var, the error will be

ERROR MESSAGE: Couldn't read file /site/ne/data/ngs/var because file does not exist

It took me a while to figure out it's due to the empty line.

Created 2013-09-26 08:51:52 | Updated | Tags: depthofcoverage gatk ensembl hgnc list

Comments (1)


I'm currently using DepthOfCoverage with -L option and a BED intervals file. I would to get gene report also. I'm not familiar with RefSeq format for the gene list.

I work with HGNC and Ensembl genes. I could get a gene list file with the following format:

HGNC chr start end

But this doesn't seem to work. Any suggestions on how I could achieve that or how I could generate a valid gene list file with my current intervals?

Thank you.