If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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..???