unrelated file

[liuhankui]

seems I put this question on the wrong page. sorry, I should put it at here; https://github.com/dbmi-bgm/granite, but I cannot find the issues button on the granite page...

Hi, i have some questions when i using novocaller, maybe someone can help me figure out some of these:

1. Can novo caller detect de novo indel?
2. when calling DNVs, the unrelated files refer to a) independent trios from the specific trios; b) samples with unrelated phenotypes that not suppose to carry DNV in this position; 3) samples that are independent of each other and the specific trios.
3. how many un-related samples will novoCaller prefer
4. we know sequencing error and gatk may detect more than one DNVs in many trios at an identical position, which is not a real DNV but a sequencing error, in case I used many other trios as un-related samples and the error DNVs in other trios at this position will increase or decrease the DNV probability
5. I saw the example vcf file, is it necessary to put the child at the first genotype column [10th column in vcf file]. the reason I ask this question is because I have many trios, if it is necessary to put the child in the 10th column in vcf file, that means I have to create many big vcf files containing similar un-related samples for each trio