Resorting chromosome order in a VCF file to match reference

[acedraper1]

Hi, thank you in advance for any help.

I am trying to re-order the chromosome order in a VCF file to match that of the reference file.

I have tried vcftools -sort, but I want my order to go back to the 'unnatural' order and this appears to only sort to the natural order.

I have also tried vcfsorter.pl, but this simply resulted in the output having the header and nothing else.

Any ideas? As simple as possible please....!

[lindenb]

use picard SortVcf http://broadinstitute.github.io/pica...w.html#SortVcf

"Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate. Can accept an external sequence dictionary. If no external dictionary is supplied, multiple inputs' headers must have the same sequence dictionaries. Multiple inputs must have the same sample names (in order)"

[acedraper1]

Thank you - that looks perfect.

I am very new at this, and just have one more question. I have downloaded and unzipped picard but can not find any examples on their github site of how to put in and execute the command for this.....

[lindenb]

Thank you - that looks perfect.

I am very new at this, and just have one more question. I have downloaded and unzipped picard but can not find any examples on their github site of how to put in and execute the command for this.....

http://broadinstitute.github.io/picard/

java -jar picard.jar SortVcf INPUT=in.vcf OUTPUT=out.vcf