GATK: sorting vcf file given a reference file

[jorge]

Hello,

I'm using GATK to call SNPs but and my reference fasta file and vcf are not in the same order.

is there a canned script that allows you sort the vcf file according to a given reference sequence?

Thanks
Jorge

[NGSfan]

Hello,

I'm using GATK to call SNPs but and my reference fasta file and vcf are not in the same order.

is there a canned script that allows you sort the vcf file according to a given reference sequence?

Thanks
Jorge

Buen dia Jorge, tengo un regalo para usted:

here you can find my script to sort a VCF by a reference genome. You'll need a *.dict file, which you can generate with Picard.

enjoy!

http://code.google.com/p/vcfsorter/

[jorge]

Hello,

Thanks a lot!

Jorge

[bioliyezhang]

Buen dia Jorge, tengo un regalo para usted:

here you can find my script to sort a VCF by a reference genome. You'll need a *.dict file, which you can generate with Picard.

enjoy!

http://code.google.com/p/vcfsorter/

very useful, thanks.

[bluesquid]

thank you!