Problems With Chromosome Ordering When Running The Gatk Indelrealigner

Question

[GPR]

Hello, I am trying to use GATK to make variant calls and have gotten stuck on IndelRealigner.

My command-line is the following: java -Djava.io.tmpdir='pwd'/tmp -Xmx5g -jar GenomeAnalysisTK.jar -I ./ input.bam -R ./ hg19.fa -T IndelRealigner -targetIntervals ./ Intervals.intervals -o out.bam -known ./ Millsand1000Ggoldstandard.indels.hg19.vcf &

I get the following error messages:

1) MESSAGE: Lexicographically sorted human genome sequence detected in reads.

<h5>ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs</h5>

2) ##### ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.

<h5>ERROR You can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam</h5> <h5>ERROR reads contigs = [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY]</h5>

I understand the 2nd error message, and am currently running ReorderSam on my bam files. I am however at odds with the 1st. error message.

Can somebody suggest/indicate what's the fix for these errors? Other than running ReorderSam in Picard Tools of course. Thanks, G.

[Alex Paciorkowski]

For error 1 I would try ReorderSam from Picard too. Why not?

Answer 1

[vdauwera]

See this article for more info on the reasons why the GATK imposes these constraints on the ordering of input files: http://www.broadinstitute.org/gatk/guide/article?id=1204

Also, you seem to be running an older version of the GATK, I strongly recommend you upgrade to a more recent version.

[GPR]

thanks for the tip!