issue with realigner target creator

Question: issue with realigner target creator

3.9 years ago by

BC357 • 70

United States

BC357 • 70 wrote:

I read about a few other people's posts concerning realigner target creator but felt that my issue couldn't be addressed after trying their approaches. Thus comes this post.

Not sure why I got the error message (see below for details), as I assumed the uploaded files were BAM files, not SAM.

Details
Issue: realigner target creator failed to execute (database build under attribute: Human Feb 2009 (GRCh37/hg19)) Source for the reference list: “History”
Selected reference file: ucsc.hg19.fasta (selecting from the Shared Data the whole GATK bundle, among which ucsc.hg19.fasta is the only one available in the dropdown)

Input file: a BAM file after running SAM-to-BAM conversion (database build under attribute: Human Feb 2009 (GRCh37/hg19))
Run with basic GATK options and basic analysis options.

Error report
##### ERROR MESSAGE: SAM/BAM file /galaxy-repl/main/scratch/tmp-gatk-brCFJ1/gatk_input.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups

Any suggestion ? Great many thanks.

realigner target creator gatk • 1.5k views

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modified 3.9 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.9 years ago by BC357 • 70

3.9 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

You'll want to add read group information to the bam. You can do this using the Picard add or replace readgroups tool: https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2Fpicard_ARRG%2F1.56.0.

ADD COMMENT • link written 3.9 years ago by Daniel Blankenberg ♦♦ 1.7k

Thank you very much for clarifying the confusion. A stupid follow-up,

(1) does the need to add/replace readgroups indicate the default BAM output has no readgroups ?

(2) according to Broad's document about realigner target creator, readgroup is "really needed". If so, is it possible to have the info of readgroup in the BAM/SAM output as a default in Galaxy ?

(3) is it possible to include programs like "ValidateSamFile" to verify if a BAM/SAM is "ready" for certain downstream analyses (I could not find such a program, although I did not do an extensive search in Galaxy either)?

(4) what's the downside of having readgroup in BAM/SAM as a default?

I apologize if some of the questions have been answered before (as there is a very steep learning curve, personally, to be able to get around with bioinformatics tools)

Thank you again for the clarification.

ADD REPLY • link written 3.9 years ago by BC357 • 70

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