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Per chromosome gVCF
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24 months ago
win • 810
India

I am using the GATK UnifiedGenotyper to generate a gVCF file based using the Emit_All_Stites option.

The problem I have is that if I have a single chromosome BAM such as BAM for only say chromosome 3 and I want gVCF data for only chromosome 3, is it possible to do that? So I want a gVCF file with variant and non variant sites only for chromosome 3

Right now when I run GATK then it starts processing all the chromosomes. Is there a way to only generate gVCF data for one chromosome even if genome truly means all the chromosomes?

gVCF GATK • 2.1k views
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4.8 years ago
David W 4.7k
New Zealand

You want the "intervals" argument 'L', as described in the docs

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The intervals argument as shown in docs it text file and so in that case how do i define a single chromosome?

The interval format is specified here

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_engine_CommandLineGATK.html#--intervals

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From the detailed description, linked from the UnifiedGenotyper page

"You can use samtools-style intervals either explicitly on the command line (e.g. -L chr1 or -L chr1:100-200) or by loading in a file containing a list of intervals (e.g. -L myFile.intervals)."

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