GATK indel realigner using custom reference

Question: GATK indel realigner using custom reference

4.3 years ago by

laura • 0

laura • 0 wrote:

I've been using some SAM (converted to BAM) files and some partial genome assemblies (custom reference sequences) to investigate variants in bulk sequences. GATK's rmdup and Realigner Target Creator had no problem with the files, but when I used them and the output of Realigner Target Creator in Indel Realigner, I got

ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:Unknown contig . . .

Additional output:

[bam_header_read] EOF marker is absent. The input is probably truncated.

The problem appears to be with the final contig in the reference sequences.

How do I correct this problem?

Thanks,

Laura

gatk custom reference indel realigner • 2.6k views

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modified 2.3 years ago by vignes.gangboard • 0 • written 4.3 years ago by laura • 0

4.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Format/loading corrections will probably resolve the issue, as most errors are linked to one of the reasons below, for any tool. The public Main Galaxy server at http://usegalaxy.org did have some downtime much earlier today, potentially in the time frame your job was running. So if that is where you are working, a straight re-run to rule out an associated job failure could be considered.

Custom reference genome troubleshooting help is here in our wiki. I am not certain from this error if that is where the problem is (GATK errors can result for a variety of reasons), but double checking fasta format is a good place to start.
http://wiki.galaxyproject.org/Support#Custom_reference_genome
http://wiki.galaxyproject.org/Learn/CustomGenomes#Troubleshooting

The BAM EOF errors can reflect a problem with incomplete data loading (but not always). Still, if you are incorporating a newly uploaded file, use FTP and confirm a successful load.
http://wiki.galaxyproject.org/Support#Loading_data

And just in case this is a factor, make certain that all input data is a match for the the genome used. In particular, the chromosome identifiers must be an exact match in order for tools to function correctly (any that make use of a reference genome, custom or native to the instance). Odd errors or results can be produced when there is a mismatch.
http://wiki.galaxyproject.org/Support#Reference_genomes

Best, Jen, Galaxy team

ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

4.3 years ago by

laura • 0

laura • 0 wrote:

Thanks, Jen. I vaguely remembered that the reference needed something done to it, but was perplexed that the problem only surfaced with the downstream tool. I'll try sorting.

Laura

ADD COMMENT • link written 4.3 years ago by laura • 0

Hi Laura, Sorting would be important. You may know this but just in case: when using GATK, follow their tool-specific sort practices described in the FAQ: http://www.broadinstitute.org/gatk/guide/article?id=1204 The GATK forum is linked from the GATK tool forms, but I'll add a new comment to our wiki as well. Jen, Galaxy team

ADD REPLY • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k

2.3 years ago by

vignes.gangboard • 0

vignes.gangboard • 0 wrote:

Determining (small) suspicious intervals which are likely in need of realignment (see the RealignerTargetCreator tool) Running the realigner over those intervals

ADD COMMENT • link written 2.3 years ago by vignes.gangboard • 0

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