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Thread Tools |
06-08-2011, 11:32 AM
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#1 |
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Member
Location: Madrid, Spain Join Date: Jun 2011
Posts: 25
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GATK: sorting vcf file given a reference file
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 |
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08-24-2011, 09:34 AM
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#2 | |
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Senior Member
Location: Austria Join Date: Apr 2009
Posts: 181
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Quote:
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/ |
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08-25-2011, 12:03 AM
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#3 |
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Member
Location: Madrid, Spain Join Date: Jun 2011
Posts: 25
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Hello,
Thanks a lot! Jorge |
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01-26-2013, 06:08 PM
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#4 | |
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Member
Location: Boston, MA Join Date: Mar 2011
Posts: 19
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Quote:
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01-14-2015, 01:16 PM
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#5 |
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Junior Member
Location: UK Join Date: Aug 2012
Posts: 3
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thank you!
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| Tags |
| fasta, gatk, reference, vcf |
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