Per chromosome gVCF

Question

[win]

I am using the GATK UnifiedGenotyper to generate a gVCF file based using the Emit_All_Sites 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?

Answer 1

[David W]

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

[win]

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.

[David W]

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).