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why is 3122x coverage not called 0/0 but ./.
I was running GENOTYPE_GIVEN_ALLELES and found some ./. calls that should be 0/0?
For example, this command
E:\GamidorFirst\Alignment_1\20161130_152325>java -jar "E:\GenomeAnalysisTK.jar" -T UnifiedGenotyper -R E:\genome.fa -I 1035_S7.bam -o 1035_S7.bam.chr2.241816967.vcf --downsampling_type NONE --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles E:\Gamidor\chr2.241816967.vcf.gz --output_mode EMIT_ALL_SITES -L E:\Gamidor\chr2.241816967.vcf.gz
Resulted in this variant
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1035-3008
chr2 241816967 . GC CG . . DP=3120;MQ=49.57 GT ./.