Hi there,

I am doing alignment using Novoalign and using best GATK (version 3.5) practice to call variant. Sample is NA12878. One of my expected variant at location chrX:31219271 is not called.

1. I ran Haplotype caller with -bamout option and i see reads (Total 100, reference 17, alternate 83) aligned in that region. Attached is the screen shot.

2. I ran samtools mpileup to check base qv on bamout.bam created with haplotype caller and here is the output -

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878a_S24_combined_001 HC

X 31219271 . C T,<*> 0 . DP=100;I16=0,17,0,83,561,18513,2708,90492,1020,61200,4980,298800,425,10625,807,11641;QS=1,1,0;VDB=1.52597e-22;SGB=54.7586;RPB=7.92804e-10;MQB=1;BQB=0.598053;MQ0F=0 P219,250,0,219,250,219 0,51,170,51,170,170

1. Mapping QV looks good

Any thoughts on why haplotyper is missing this variant ?

Thanks,

Swati