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Hello
Thanks a lot for the program. I'm trying to call de novo variants in my trio, its normal takes 5 days? with Varscan just takes 1-2 hours.
Thanks
ccs76 updated
4 years ago
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Hi Chapmanb,
scalpel is missing one library and fail
Thanks!
Genotyping with Scalpel
[2015-08-24T22:11Z] Local date and time: Mon Aug 24 22:11:42 2015
[2015-08-24T22:11Z]
[2015-08-24T22:11Z] Progra…
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@vdauwera commented on [Mon Nov 14 2016](https://github.com/broadinstitute/gatk-protected/issues/777)
This derives from a bug report in GATK 3.5 where we found that using -allowNonUniqueKmersInRef re…
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Hello,
I'm attempting to annotate a vcf produced by GATK's haplotype caller using the following command:
`##GATKCommandLine=`
Some of the resulting vcf records, when run through annovar have t…
Tvira updated
5 years ago
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After testing with the latest release (1.10) we've encountered an error when using bcftools view and filter:
`chr1 17000202 . A C . clustered_events;haplotype;normal_artifact;strand_bias CONTQ=64;D…
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Hi,
I am trying to test what is the minimum read coverage that can still be considered identifying information for a sample, starting by testing my own data.
I *could* successfully identify my o…
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It looks like gnomad_popmax_af doesn't match for some variants
https://gnomad.broadinstitute.org/variant/1-16902804-C-A gnomad_popmax_af looks to be 0.01492
Yet following gnotate with the grch37…
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Hi,
I've used bcbio to run some WGS data and perform validation with NA12878 for the genome ( callable bed) and exome ( our target file ). I was a bit surprised by the results as the analysis was i…
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I tried SpliceAI and the results are all like this: SpliceAI=C|.|.|.|.|.|.|.|.|.
The vcf file is generated from the GATK packages by analyzing a WES data. Please suggest the solution. Thanks!
Here…
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Running this pipeline
https://github.com/macarthur-lab/hail-elasticsearch-pipelines/blob/master/luigi_pipeline/seqr_loading.py#L39
on a non-Broad VCF with this header and several example variants:
…