Loss of variants
I am using GenomeAnalysisTK-2.3-9. For performing a GATK Multisample call I have a work flow like this:
(1) Make GATK Multisample call over N samples
(2) Perform Recalibration on the multisample result from previous set
(3) Apply Recalibration
(4) Combine variants from several batches going through step 1 to 3
(5) Genotype call against single samples now using the master VCF from step 4
(6) Finally combining all variants from the single sample calls from step 5
Now, when I check the Master VCF from step 4 and the final result after step 6, I see that some variants are missing in the end result though they passed the recalibration step and having a allele frequency greater than 0.8.
Shouldn't all the variants from step 4 have been included in the final merged VCF in step 6?