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.
AD value higher than the DP value
Calling SNPs using a single bam file with the command:
java -Xmx30g -jar GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R ref.fasta \ -I input.bam \ -o output.vcf \
and when looking at the output file, most DP values were equal to the AD values and in few cases the AD value was higher. Thought that AD values are the unfiltered counts of all reads and DP fields describes the total depth of reads that passed the Unified genotyper’s internal quality control. Is it normal for the AD values to be higher than the DP value?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT eo227 gi|218430358|emb|CU928163.2| 2317180 . T G 76.55 . AC=1;AF=0.50;AN=2;BaseQRankSum=1.568;DP=10;Dels=0.00;FS=11.181;HRun=0;HaplotypeScore=15.8585;MQ=28.63;MQ0=0;MQRankSum=1.036;QD=7.66;ReadPosRankSum=-0.633;SB=-0.01 GT:AD:DP:GQ:PL 0/1:6,4:10:99:107,0,154 gi|218430358|emb|CU928163.2| 2317181 . T G 71.96 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.550;DP=10;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=19.8574;MQ=28.63;MQ0=0;MQRankSum=-1.754;QD=7.20;ReadPosRankSum=-1.754;SB=-0.01 GT:AD:DP:GQ:PL 0/1:3,4:10:87.90:102,0,88