Question: Beagle 4.0 Imputation - Warning: Skipping VCF record with no data
0
gravatar for Wietje
5 months ago by
Wietje120
Wietje120 wrote:

Hello fellow Biostars,

I am currently working on an imputation from 6k to 50k data and one of the programmes in use is Beagle 4.0 (since I want to integrate pedigree data). When I performed a test run on a single chromosome, the following warning came up for 456 out of 986 SNPs:

"Skipping VCF record with no data" ---> Do you have any idea how this can happen?

I checked the manual/ documentation and other platforms and couldn't find any other comparable reports. Interestingly, the imputation was performed nevertheless and the accuracy seems to be very good as well. Still, I would like to get to the bottom of this problem/ warning.

All help and ideas are heartily appreciated!

ADD COMMENTlink modified 5 months ago by Pierre Lindenbaum107k • written 5 months ago by Wietje120
0
gravatar for Pierre Lindenbaum
5 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum107k wrote:

called here: https://github.com/tfwillems/PhasedBEAGLE/blob/master/vcf/VcfWindow.java#L341 when e.isMissingData()

defined here: https://github.com/tfwillems/PhasedBEAGLE/blob/master/vcf/VcfEmission.java#L70

Returns 'true' if the genotype emission probabilities for each sample are determined by a genotype that contains only missing alleles, and returns 'false' otherwise. Return 'true' if the genotype emission probabilities for each sample are determined by a genotype that contains only missing alleles, and 'false' otherwise.

ADD COMMENTlink written 5 months ago by Pierre Lindenbaum107k
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