Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
Confusion in using gVCF mode
I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems:
1- Should we run gVCF even when we have one WES sample?
2- I have 3 WES samples, should I use gVCF --> Cosolidate --> GenotypeGVCF --> VCF or it is better to obtain VCF directly from HaplotypeCaller and ignore its next steps?
3- If I have 3-5 WES samples, is it better to run HaplotypeCaller with multiple input (bams) or separately?