GATK RealignTargetCreator compatibilities

[gwilymh]

Hi,

I have been trying to use the GATK RealignTargetCreator function via the Galaxy server to identify putative INDEL regions in a sequence alignment for downstream use in the GATK IndelRealigner function. No matter what I do, however, I keep getting error messages: Index file /space/g2main/tmp-gatk-ZsBUBG/gatk_input.fasta.fai does not exist but could not be created because: . File /space/g2main/tmp-gatk-ZsBUBG/gatk_input.fasta is malformed: An invalid line was found in the contig: Chr1

The BAM/SAM files I am trying to use were generated in Geneious from aligning Illumina NG sequence reads against a reference genome. The reference genome I am using is in the form of a FASTA file which was downloaded from the USCS website.

Does anyone know if there is some kind of incompatibility between GATK, Geneious or Illumina sequences?

[Bukowski]

Does the BAM have the chromosomes labelled 1..22,X,Y and the fasta file you're using have them named chr1..chr22,chrX,chrY perhaps?

[adaptivegenome]

also make sure the order of the chromosomes is the same