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?
I am learning to use the DepthofCoverage function to obtain the gene coverage information for a collection of bacterial contigs that were mapped with metagenomic reads. The original post introducing this function is here: http://gatkforums.broadinstitute.org/discussion/40/depthofcoverage-v3-0-how-much-data-do-i-have#latest
In the post, you mentioned the gene list, as follow:
-geneList /path/to/gene/list.txt The provided gene list must be of the following format: 585 NM_001005484 chr1 + 58953 59871 58953 59871 1 58953, 59871, 0 OR4F5 cmpl cmpl 0, 587 NM_001005224 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F3 cmpl cmpl 0,
I have three inquiries:
Thanks so much!