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Old 11-05-2013, 08:18 AM   #3
rzeng
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Location: houston

Join Date: Aug 2013
Posts: 19
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BW. thank you for the information!

Is -A: allelic depths which is the number of AD like example below that allelic depth is 0+2 =2 then I can set -A as a number based on the AD?

GT: AD: DP:GQ:PL 1/1:0,2:2:6:66,6,0


Also I do not quite understand what was the -resource my_dbsnp,vcf dbsnp135_path.vcf -E my_dbsnp.infofieldname -resource:my_snps2,vcf my_snps2_path.vcf -E my_snps2.infofiledname1 -E my_snps2.infofieldname2 -comp my_snps2, vcf my_snps2_path.vcf exactly mean?

Suppose that my sample variant data is input1.vcf and I have other 5 extra variant data as input2/input3/input4/input5/input6.vcf and the i type
--variant input1.vcf and type -resource like follows??

-resource input2.vcf input2_path.vcf -E input2.infofildname
-resource input3.vcf input3_path.vcf -E input3.infofildname
.........

What is -comp my_snps2 mean? I could not find a clear explain for this in GATK annotation argument details.



Quote:
Originally Posted by bw. View Post
You can use the GATK VariantAnnotator .

So something like:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator
-R mm9.fa
--variant input.vcf
--dbsnp dbsnp135_path.vcf
-A DepthPerAlleleBySample # you can run with --list to see other -A options
-resource:my_dbsnp,vcf dbsnp135_path.vcf -E my_dbsnp.infofieldname
-resource:my_snps2,vcf my_snps2_path.vcf -E my_snps2.infofiledname1 -E my_snps2.infofieldname2 -comp my_snps2, vcf my_snps2_path.vcf
-o output.vcf


This will produce output.vcf which has all the variants in input.vcf along with additional INFO field values based on values from the other .vcf files.
It should then be possible to use GATK SelectVariants (or some other filtering tool) to extract the variants that you want.

GATK tools can be somewhat complicated to use, so there's also this list:
http://nickloman.github.io/2013/01/1...ing-vcf-files/

Last edited by rzeng; 11-05-2013 at 08:25 AM.
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