Entering edit mode
8.5 years ago
a.james
▴
240
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..
See VCF spec. AF is the alternate allele frequency.
The AF field from the VCF file is the theoretical allele frequency that corresponds to the genotype call made by the tool.