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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.

Created 2012-10-22 17:31:20 | Updated 2012-10-22 18:22:28 | Tags: depthofcoverage refseq
Comments (3)


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:

  1. Can you please provide headers to the values in each column?
  2. I am working with bacterial genomic contigs, can you please specify what basic information is needed for a gene list (e.g., name of contig, name of gene, location of gene in the contig, from... to ..., etc.)?

Thanks so much!