SkyWarrior
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Activity overview
Latest activity by SkyWarrior-
SkyWarrior commented,
You may want to download and see it yourself. There is no single file format for this resource and some require internet connection. gs://broad-public-datasets/funcotator/funcotator_dataSources.v1...
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SkyWarrior commented,
Hi Rami Kheireddine I am not sure if there is any available zebra fish resources for Funcotator. You may wish to compile one for yourself but I would suggest you try Snpeff or Variant Effect Predic...
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SkyWarrior commented,
Sorry my bad. You may use 1000G whole genome samples if you wish. Just make sure that they were also processed with the same reference genome of yours. I used to do that and I even included some of...
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SkyWarrior commented,
Hi paalmbj Short answer: Don't even bother. Long and convoluted answer: There may be a duct tape solution you may try. Check 1000G whole exome files however the capture kit compatibility will be a...
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SkyWarrior commented,
Hi Tamer Mansour 1200 GVCF files immediately tells me that you need GenomicsDBImport to collect them together. This gives you a main advantage of ability to add more and more samples later on to yo...
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SkyWarrior commented,
Hi Marcela Martinez Inside the DetermineContigPloidy output folders per sample there is a file named contig_ploidy.tsv. That file has all the ploidy estimators per contig for your samples. To be s...
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SkyWarrior commented,
Here is the code for the SplitIntervals. It is in the code actually. I am using IntervalListTools for this purpose. #Run Scatter intervals. If it was run before clear the previous ones and recreat...
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SkyWarrior commented,
I know that this is totally out of scope for GATK and its accessory partners such as cromwell and wdl but for the sake of getting an answer I will post my perl script here with details. You are fre...
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SkyWarrior commented,
My question is if you will use all shards all at the same time in the same GermlineCNVCaller step why would you create them anyway. A single interval_list would suffice and it will create a single ...
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SkyWarrior commented,
Hi Y R --sample-index is not based on shards but based on the order and the number of samples processed in GermlineCNVCaller step. If you have 200 samples you need to start your --sample-index from...