GATK GenotypeGVCFs explain

Question

[Nobody]

Hello,

Could you explain to me what GentypeGVCFs does and what it gives in output.

Thank you.

[Pierre Lindenbaum]

GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.

[Nobody]

what does the option L

[raphael.B]

It limits the operation to some genomic regions given as parameter

[Nobody]

thank you

[Pierre Lindenbaum]

https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists

[Nobody]

thank you all !

Answer 1

[Zeng Jingyu]

The official explaination of GenotyeGVCF is here (4.1.5.0), as the document said it has two types of working mode, for multiple samples and single sample.

I think the GATK document is sufficient for you to know about the function.