I am carrying out Exomeseq analysis for trio (Son is affected, Father is affected, Mother is unaffected). I did following steps
Trimmed using Trimmomatic
Aligned using BWA mem, Sorted, Marked Duplicates and Recalibrated.
For all 3 samples the coverage for target bases at 20X - 92%, at 30X - 86%, 40X - 80%, 50X - 72% (Is this coverage good enough for exome sequencing?)
Variant calling using Unified Genotyper - GATK ( Is Unifiedgenotyper good for Trio analysis?)
Got raw variants (900,000), Filtered variants, Annotated with SnpEff
Selected PASS variants (750,000), Selected Exonic Variants (12,000)
Then I checked in disease-related genes (Got 15 variants)
Finally, I selected common variants between affected son and affected father ( 3000 Heterozygous and 2800 Homozygous alternate variants)
Planning to check in DBSNP.
What are the other general ways to reduce my variants?