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VCF file and allele frequency
I am using I am using GATK RNA-seq variant pipeline for finding muttaion/vatiants on the list of gene given in teh follwoing 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.
I AF means allele frequency or it has to be calculated separately from VCF file and if so how can I do it..???