Test-drive the GATK tools and Best Practices pipelines on Terra
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A bug in snp results from Haplotyper
I took use Haplotyper to get snp.vcf results.
There 's a snp is strange:
chr2 29448423 . T G 299.77 PASS AC=1;AF=0.500;AN=2;DP=114;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;QD=2.63 GT:AD:GQ:PL 0/1:114,0:99:328,0,13034
Both DP and AD are 114;
Depth of reference is also 114.
Isn't this position 0/0 ?
Is this a bug for Haplotyper ?
I checked bam files and found that there were 119 reads covering this position.
114 for T
5 for G
Why is the information of these 5 reads supporting G missing?
Thank you ~