I have problems with the GATK IndelRealigner. I run GATK version 1.0.5365
Except the standard input and output files I use:
-compress 0
-L chr_number
-B:indels,VCF dbSNP_indelfile.vcf
The pipeline I use look like this:
1. Split fastq-files into smaller parts (paired-end)
2. Align each parts with BWA
3. sort each part with samtools
4. merge with samtools
5. run GATK -T IndelRealigner on each chromosome (after RealignerTargetCreator of course)
All chromosomes except number 11 is going ok.
In chr11 I get this error:
java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment for /glob/jonasc/alignment_test2/pipe_line_test_sorted_realign.bwa.11.bam. Sort order is coordinate. Offending records are at [11:51571970] and [11:51571888]
Using samtools view on the region in the input bam-file I can see that the reads are sorted.
Any help to solve this would be useful.
Except the standard input and output files I use:
-compress 0
-L chr_number
-B:indels,VCF dbSNP_indelfile.vcf
The pipeline I use look like this:
1. Split fastq-files into smaller parts (paired-end)
2. Align each parts with BWA
3. sort each part with samtools
4. merge with samtools
5. run GATK -T IndelRealigner on each chromosome (after RealignerTargetCreator of course)
All chromosomes except number 11 is going ok.
In chr11 I get this error:
java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment for /glob/jonasc/alignment_test2/pipe_line_test_sorted_realign.bwa.11.bam. Sort order is coordinate. Offending records are at [11:51571970] and [11:51571888]
Using samtools view on the region in the input bam-file I can see that the reads are sorted.
Any help to solve this would be useful.
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