How to get heterozygotes SNP with HaplotypeCaller ?
I am new to GATK, I try to find SNPs for paired-end data in the mosquito. The genome of the mosquito many polymorphism.
I try to get a VCF file for each position all posibility for a SNP. In fact, when I look at my VCF file I have only one posibility for SNP as often it is heterozygous.
R 86 . T A 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=0.000;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.84;MQRankSum=-2.369;QD=9.22;ReadPosRankSum=0.992;SOR=0.368 GT:AD:DP:GQ:PL 0/1:5,3:8:99:102,0,188
At this position, with IGV i can see an heterozygous SNP : some reads are A other are T like the reference. Is it possible to get this information ?
This is my command line :
java -Xmx8g -jar GenomeAnalysisTK.jar -nct 4 -T HaplotypeCaller -R ../GENOME/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa -I ../RESULTS/NJ3-5302_2016-09-30/MAPPING_NJ3-5302.sorted.bam -o ../RESULTS/NJ3-5302_2016-09-30/test.vcf -mbq 25 -gt_mode DISCOVERY -L 2R:1-500000