Question: Why do I see 0|0 genotypes in my Long Ranger output?
Answer: If you are using Freebayes as the variant caller in Long Ranger you are likely to see a small number of 0|0 or 0/0 genotypes. This phenomenon is discussed in more detail on the Freebayes github site here.
Our publicly available NA12878 data set here was run with Long Ranger 2.1.4 using Freebayes as a variant caller. It has several thousand 0|0 genotype calls.
Starting with Long Ranger 2.2.1 GATK became our recommended variant caller.