Question: Minor Allele Frequency calculation from VCF file
0
gravatar for a.james
2.1 years ago by
a.james110
Germany
a.james110 wrote:

 

Hello All

I am using GATK RNA-seq variant pipeline for finding mutation/variant calling on the list of gene given in the following command line

java-1.7 -jar -Xincgc -Xmx1586M GenomeAnalysisTK-3.2-2.jar -T HaplotypeCaller --filter_reads_with_N_cigar -R human_genome37_gatk.fa -D dbsnp_137.hg19.vcf -I sample_split.bam -o sample.vcf -L mylist.intervals

And the resulting VCF files has for variants AF either 100 % or 50 % . It would be great if anyone would explain me what does AF means in INFO column from VCF file. example,

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    sample
chr1    564598    rs6594028    A    G    15123.77    .    AC=2;AF=1.00;AN=2;DB;DP=392;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.09    GT:AD:DP:GQ:PL    1/1:0,389:389:99:15152,1167,0
chr1    564654    rs147404388    G    A    15595.77    .    AC=2;AF=1.00;AN=2;DB;DP=422;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.40    GT:AD:DP:GQ:PL    1/1:0,419:419:99:15624,1255,0
chr1    564862    rs1988726    T    C    476.77    .    AC=2;AF=1.00;AN=2;DB;DP=11;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.66    GT:AD:DP:GQ:PL    1/1:0,11:11:36:505,36,0

 

It would be great if someone could share how to calculate Allele frequency from the VCF file.. 

snp rna-seq • 2.8k views
ADD COMMENTlink modified 2.1 years ago by EagleEye4.8k • written 2.1 years ago by a.james110
2

See VCF spec. AF is the alternate allele frequency.

ADD REPLYlink written 2.1 years ago by lh330k

The AF feild from the VCF file is the theoretical allele frequency that corresponds to the genotype call made by the tool. 

ADD REPLYlink written 2.1 years ago by a.james110
2
gravatar for EagleEye
2.1 years ago by
EagleEye4.8k
Sweden
EagleEye4.8k wrote:
http://samtools.github.io/hts-specs/VCFv4.1.pdf http://samtools.github.io/hts-specs/VCFv4.2.pdf
ADD COMMENTlink written 2.1 years ago by EagleEye4.8k
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