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Getting very less entries in vcf file??
I Run Unified genotyper for identify the indels and deletion.
I used Realigner target creater got forIndelRealigner.intervals. used this output for Indel Realigner and get the output bam file which i gave as input toUnified Genotyper.
I got result as
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BRCA1
gi|262359905|ref|NG_005905.2| 48155 . G A 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.466;DP=47;Dels=0.00;FS=2.721;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.31;MQ0=0;MQRankSum=-4.812;QD=8.25;ReadPosRankSum=0.535 GT:AD:DP:GQ:PL 0/1:25,22:45:99:416,0,676
But if i run without these steps (Realigner target creater, Indel Realigner) i am getting the same output.
Also i used the same dataset and run it in samtools and got more SNP.
I am looking for a deletion in the dataset.
I would like to get the result from GATK Could you please suggest on the same.