Error with Demo

[choishingwan]

Hi there, when trying to run the demo by typing ./bash_run, I found that there's an error in the output. Upon checking, it is because the demo will generate a vcf containing the sample name instead of SAMPLE which was used in the header of the expected result. Maybe you will have to change the header of the expected result such that it will no longer give such warning.

Also, when reading the read me, the document suggest that the demo should be running on two samples NA12891 and NA12892. However, I couldn't find any trace of the NA12892 sample nor do I know how to perform multi-sample calling. Is it possible to perform multi-sample calling or is it not intended?

Thank you for your time and programme

[ctsa]

Thanks for reporting these issues -- they should be fixed now. I updated the expected result and changed to README to drop the reference to NA12892 -- this was in the demo written for strelka, but does not describe the subset of demo data used for Isaac variant caller.

[choishingwan]

Hi, so does that mean that for ISAAC, we cannot perform multi-sample calling? As for other variant caller, they all mention that it is better to call the samples together so we are not sure if we should also do this for iSAAC. At the same time, we found that the output from iSAAC seemingly incompatible to other down-stream analysis tools such as GATK, is there any options that we may set to make it compatible?

Thank you

[ctsa]

IVC is designed to call individual samples. Any specific issues you've encountered due to ouput which does not follow the written (or de-facto) VCF spec can be reported here. You should be aware that many tools are not designed to scale up to a VCF input which contains all non-variant sites (such as gVCF), you might find this documentation helpful:

https://sites.google.com/site/gvcftools/home/about-gvcf