Question

GATK GenotypeGVCFs explain

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13 months ago

Nobody ▴ 30

Hello,

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

Thank you.

calling gatk variant GenotypeGVCFs • 1.6k views

ADD COMMENT • link 13 months ago by Nobody ▴ 30

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

ADD REPLY • link 13 months ago by Pierre Lindenbaum 161k

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what does the option L

ADD REPLY • link 13 months ago by Nobody ▴ 30

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It limits the operation to some genomic regions given as parameter

ADD REPLY • link 13 months ago by raphael.B ▴ 520

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thank you

ADD REPLY • link 13 months ago by Nobody ▴ 30

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

ADD REPLY • link 13 months ago by Pierre Lindenbaum 161k

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thank you all !

ADD REPLY • link 13 months ago by Nobody ▴ 30

score 1 · Answer 1 · 2023-03-22

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13 months ago

Zeng Jingyu ▴ 60

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.

ADD COMMENT • link 13 months ago by Zeng Jingyu ▴ 60