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rare variant missing in the vcf file crang Bioinformatics 10 04-04-2013 08:27 AM

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Old 02-10-2014, 11:52 AM   #1
rohan_1925
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Default Rare variants from annotated vcf file

Hi,

I have annotated my vcf file of 20 samples from GATK's 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?
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Old 02-11-2014, 12:34 PM   #2
m_two
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You may want to download the dbSNP VCF file containing the 1000 Genome's project minor allele frequencies.
ftp://ftp.ncbi.nlm.nih.gov/snp/organ...uman_9606/VCF/

You can use joinx to process the data:
https://github.com/genome/joinx


##INFO=<ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
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Old 02-11-2014, 12:35 PM   #3
m_two
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In addition, this may be useful: http://evs.gs.washington.edu/EVS/
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gatk unifiedgenotyper, variant analysis, variant filtering, variantannotator

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