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!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

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!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
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.

Grouping duplicate reads together

brain_foodbrain_food Member Posts: 2

Hello,
I've been using the Picardtools MarkDuplicates tool. I'd like to identify which reads are duplicates of each other (ie. if read.1234 is a duplicate of read.5678, I want to be able to retrieve this relationship). Does the MarkDuplicates output indicate this in any way? While I could group reads together if they share the same start coordinate listed in the BAM file, this gets a little tricky if the reads align to the minus strand, or if there are mismatches in the first couple of nucleotides in the read. I think the MarkDuplicates program must be collecting this information behind the scenes when it's finding duplicates. Thank you very much for your help.

Best Answer

Answers

Sign In or Register to comment.