GATK error

[poisson200]

java -jar gatk -T IndelGenotyperV2 -l INFO -bed brief.bed -R /data/results/genomes/hg18/hg18.fa -I fastq.sorted.realigned.bam -o fastq_indel.txt -verbose fastq_indel_statistics.txt

This produces an error
"GenomeLocParser are incorrect:The stop position 1 is less than start 141481674"

does anyone know how to solve?


INFO 20:34:49,281 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,283 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5974, Compiled 2011/06/10 13:26:59
INFO 20:34:49,283 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 20:34:49,283 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 20:34:49,283 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 20:34:49,284 HelpFormatter - Program Args: -T IndelGenotyperV2 -l INFO -bed brief.bed -R /data/results/genomes/hg18/hg18.fa -I fastq.sorted.realigned.bam -o fastq_indel.txt -verbose fastq_indel_statistics.txt
INFO 20:34:49,284 HelpFormatter - Date/Time: 2011/06/16 20:34:49
INFO 20:34:49,284 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,284 HelpFormatter - ---------------------------------------------------------------------------
INFO 20:34:49,295 GenomeAnalysisEngine - Strictness is SILENT
INFO 20:36:05,521 IndelGenotyperV2Walker - No gene annotations available
INFO 20:37:25,387 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 20:37:25,388 TraversalEngine - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 20:37:25,392 TraversalEngine - chr1:18958321 1.00e+00 79.9 s 132.1 w 0.6% 3.6 h 3.6 h
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.0.5974):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 1 is less than start 141481674
##### ERROR ------------------------------------------------------------------------------------------

[ulz_peter]

As far as I know bwa merges the reference sequences for aligning the reads. It somehow sounds as if there is a read which maps between two sequences. If this is the case you could clean the sam file by using cleanSam from picard.

[fpepin]

I'm actually having the same problem as well. CleanSam doesn't help in this case. Picard's ValidateSamFile does show multiple errors that I think are related:

Mate unmapped flag does not match read unmapped flag of mate
Mate not found for paired read

Interestingly, using an older version of GATK (1.0.5777 in my case) works well, so I'm thinking it's just an issue of GATK being more stringent than it used to be.

I'm hoping that Picard's FixMateInformation can fix it as I'd rather not be stuck with an older version of GATK, but at least we know that using the older version works.

[poisson200]

Hi,
Sorry, it was a while ago but I think I solved this by checking out latest version of GATK from cvs (rather than download the one from their website). Also...

# Needs the human genome to be sorted karyotypically. I did this by downloading from GATK site
# You need to make a samtools faidx and a Picard (CreateSequenceDictionary.jar) .dict file for re-ording your bam file GENOME NEEDS A DICT AND FAIDX FILES