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Question about using expression in VariantAnnotator

Hi, I am trying to add CAF (comma delimited list of allele frequencies) from dbSNP to VCF file using VariantAnnotator. However, I am only getting one of the two frequencies in the output. How can I get the complete list of frequencies from the CAF field?

My VCF (dbsnp.CAF=0.3119)

1       69897   rs200676709     T       C       2132.77 .       AC=2;AF=1.00;AN=2;BaseQRankSum=-3.176;ClippingRankSum=0.000;DB;DP=92;ExcessHet=3.0103;FS=30.719;MLEAC=2;MLEAF=1.00;MQ=28.41;MQRankSum=-1.111;QD=23.18;ReadPosRankSum=0.081;SOR=2.143;dbsnp.CAF=0.3119

dbSNP (CAF=0.3119,0.6881)

1       69897   rs200676709     T       C       .       .       RS=200676709;RSPOS=69897;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050300000305170026000100;GENEINFO=OR4F5:79501;WGT=1;VC=SNV;S3D;SLO;REF;SYN;ASP;VLD;G5A;G5;KGPhase3;CAF=0.3119,0.6881;COMMON=1
Args: -T VariantAnnotator -R human_g1k_v37_decoy.fasta --resource:dbsnp dbsnp.vcf.gz -E dbsnp.CAF --resourceAlleleConcordance --variant gatk.vcf --out with-dbsnp.vcf

Using GATK v3.6-0-g89b7209

Issue · Github
by Sheila

Issue Number
1420
State
closed
Last Updated
Milestone
Array
Closed By
chandrans

Answers

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