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# Rare variants from annotated vcf file

New YorkMember Posts: 5
edited February 2014

Hi,

I have annotated my vcf file of 20 samples from Unified genotyper using the following steps.

Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator

My question is how should I proceed if I have to select rare variants (MAF<1%) for the candidate genes that I have,for each of these 20 samples?

Post edited by rohan1925 on
Tagged:

edited February 2014

Hi there,

If you're asking how you should design your analysis, I'm afraid this question is beyond our current scope of support. I can only point you to the variant manipulation tools (e.g. SelectVariants) and answer specific questions about how to use them.

Geraldine Van der Auwera, PhD

• New YorkMember Posts: 5
edited February 2014

I want to use SelectVariants only since I have used all the tools from GATK until Variant Annotator for variants.So in this how should I get MAF (minor allele frequency) to be less than 1%,using -AF parameter?

Also,I need to select variants only for candidate genes that I have.

Ah, sorry to get back to you so late. I believe you should be able to do that simply using -select "AF < 0.01". Let me know if that doesn't work for you.

Geraldine Van der Auwera, PhD

• New YorkMember Posts: 5

Hi,

Thanks for your response! I am using this command,and getting some error.

java -Xmx2g -jar /GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -T SelectVariants -R human_g1k_v37.fasta --variant annotated.vcf -o annotated.select.vcf -select "AF<0.01"

##### ERROR stack trace

java.lang.IllegalArgumentException: Invalid JEXL expression detected for select-0 with message ![0,9]: 'AF < 0.01;' < error

-an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum

Do I have to include -an AF as well?

No, if it was a problem of missing annotations the error would be different. Is there any chance some of your variants are multi-allelic? The problem is that for multi-allelic variants, AF is a list of numbers instead of a single number, so the JEXL expression I gave you won't work. Unfortunately there is currently no way to test AF for multi-allelic variants, so you need to skip them in order for this to work.

Geraldine Van der Auwera, PhD