When trying to call variants I get the error message:
##### ERROR MESSAGE: Lexicographically sorted human genome sequence detected in reads. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1328for more information. Error details: 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]
Both my fasta file and my bams have the chromosomes sorted in this order. Therefore I need to re-sort my bams and possibly my fasta to be in numerical order: chr1,chr2 etc.
However, due to the chr in the chromosome name samtools sort does not sort the chromosomes into the desired order. Can anyone help with this sorting?