Incompatible contigs No overlapping contigs found.

Question

[manojkumarbioinfo]

I have used the flowing command for GATK Relaigner target creator while running this command I am ending with the error message as shown below

Command

java -XX:-DoEscapeAnalysis -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fasta -I bwa_mem_RG.bam -known Mills_and_1000G_gold_standard.indels.b37.vcf -o Aln.intervals

ERROR MESSAGE:

Input files /home/bioinformatics/Documents/Ocular tumor/Sample9/Mills_and_1000G_gold_standard.indels.b37.vcf and reference have incompatible contigs: No overlapping contigs found.
##### ERROR   /home/bioinformatics/Documents/Ocular tumor/Sample9/Mills_and_1000G_gold_standard.indels.b37.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y]
##### ERROR   reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]

I tried to sort my reference genome still it shows the error.

Answer 1

[Chris Cole]

Look at the error message.

The data in Mills_and_1000G_gold_standard.indels.b37.vcf has chromosomes labelled as: 1, 2, 3, etc. Whereas your data 'reference' has chromosomes labelled as: chr1, chr2, chr3, etc. GATK doesn't know that they refer to the same thing.

Welcome to the world of stupid, conflicting naming conventions in biology.

You will need to change one or other so that all the chromosome names are the same. E.g. in hg19.fasta, bwa_mem_RG.bam and Mills_and_1000G_gold_standard.indels.b37.vcf.