The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

DepthOfCoverage for whole genome: skipped few regions

NeelamNeelam BlacksburgMember Posts: 6

I used following command to get coverage data for entire genome:
java -Xmx2g -jar ~/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -T DepthOfCoverage -R ~/Gmax_189.fa -o DoCov_dedup -I dedup.bam.list

Coverage was not reported for 36025109 bases. Many skipped bases fall one after another in the genome to form big continuous regions. I do not understand, why these regions were skipped. Usually if there was no mapping, the coverage value should be reported as 0.

Appreciate some insight into this issue! Thank you.

Tagged:

Best Answers

Answers

  • NeelamNeelam BlacksburgMember Posts: 6

    Thank you. Those are all strings of ambiguous bases. What will be the situation for single ambiguous base in middle of canonical bases?

  • NeelamNeelam BlacksburgMember Posts: 6

    I found DepthOfCoverage is reporting for ambiguous bases in coverage output file.
    Attached are the snapshots of: (1) coverage output for small region on chromosome 1;
    image

    and (2) alignments output in this region.
    image

    Position #21956 is starting of ambiguous region that is more than 8K long in reference genome.
    How can I get rid of these points from depth output file, without actually eliminating the regions of no mapping?

Sign In or Register to comment.