How to slice a gvcf file with tabix?
I am using the following tabix command to slice a GVCF file, but it is not creating sliced GVCF files. I have a bed file for the hg38 genome reference with 1MB regions and 1kb padding, and I want to slice using the bed file. I was wondering if you could help me with how to do it?
./tabix -R regions.bed -p vcf sample.g.vcf.gz > sample_sliced.gz
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why would you need to slice a gvcf file ? all the tools in gatk can use a BED / interval / chromosome to narrow the analysis
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Pierre Lindenbaum
What is your suggestion to run GenomicsDBImport efficiently?
call the GVCF by slices eg: chr1:1000000-2000000
run GenomicsDBImport for each sample for one interval
genotype gvcf for one interval
at the end concatenate all the VCFs
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GenoMax
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Pierre Lindenbaum
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Pierre Lindenbaum
No, in haplotypecaller
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Pierre Lindenbaum
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