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                                            fatimasnc

matching chromosome order in vcf and bam files

Hi, I'm having the same problem here. I tried @raivivek's suggestion but after running `picard SortVcf` on my VCF file I still get the same error: ``` FATAL ERROR -...

matching chromosome order in vcf and bam files

Thanks a lot for your reply @raivivek! In the end we managed to solve it with [this helper script](https://github.com/aertslab/popscle_helper_tools/blob/master/sort_vcf_same_as_bam.sh) from the aerts lab :)