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genotyping CNVs

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

Hi @bhandsaker ,

I run 220 samples, 1 chromosome through the CNV discovery pipeline on recommended settings which generates this vcf gs_cnv.genotypes.vcf.gz, comprising of the metrics for each genotype and sample. I guess that I just pass this vcf in to the svgenotyper command, as for the deletion pipeline,. However, this outputs a similar file, i.e. without distinct genotype calls, 0/0, 0/1 etc. Am I doing something wrong? I didn't notice a CNV calling example in the test scripts.


Will Gilks

Best Answer


  • Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

    @bhandsaker Thanks, all that's encouraging. The phasing of CNVs and SNPs is exciting. I'm looking through Beagle now to try and understand what's required.

    I'm also trying to submit the CNV and deletion records from Genomestrip, to NCBI dbVar but the formatting of the vcf looks tricky.

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