User: cocchi.e89

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cocchi.e8980
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Posts by cocchi.e89

<prev • 89 results • page 1 of 9 • next >
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GATK Mutect2 tumor-segmentation table
... I am working on somatic calling using GATK Mutect2 and following their [best practice guidelines][1] they now have a CalculateContamination step whose example states: gatk CalculateContamination \ -I getpileupsummaries.table \ -tumor-segmentation segments.table \ ...
gatk mutect2 somatic written 1 day ago by cocchi.e8980
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WGS hg19/hg38 Panel-of-Normals (GATK SV-CNV)
... I am working on CNV calling through [GATK latest guideline][1], in order to perform the analysis there's need for a Panel-of-Normals file that can be generated from other samples. I was wondering if it possible to download these PoN files from some repository etc., I'm interested in both hg19 and ...
sv gatk pon panel-of-normals cnv written 10 days ago by cocchi.e8980
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Comment: C: GATK Mutect2 Panel-Of-Normals generation
... Looks like it did the trick. Thank you very much @WouterDeCoster ! ...
written 4 weeks ago by cocchi.e8980
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Comment: C: GATK Mutect2 Panel-Of-Normals generation
... No my samples are hg19, moreover I’d like to be sure that the PON comes from samples samples with the same kit ...
written 5 weeks ago by cocchi.e8980
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GATK Mutect2 Panel-Of-Normals generation
... I am trying to generate PON for WES samples following [GATK recommendations][1], they also have another explanation in this [Mutect2 article][2] but it's basically the same identical 3-steps procedure: > ***step 1**. Run Mutect2 in tumor-only mode for each normal sample*: ` gatk Mutect2 -R refer ...
gatk panel-of-normal non-tumor wes mutect2 written 5 weeks ago by cocchi.e8980 • updated 5 weeks ago by WouterDeCoster44k
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Answer: A: gnomAD Structural Variants pipeline usage
... Looks like they published an updated and commented repo here: https://github.com/broadinstitute/gatk-sv ...
written 6 weeks ago by cocchi.e8980
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gnomAD Structural Variants pipeline usage
... I am trying to use the recently published [gnomad-SV calling pipeline][1] for structural variant calling. They released all code in [github][2] and it basically works through *.wdl* scripts that can be deployed on [Terra Firecloud][3] and each of this script looks like calling a docker image that op ...
sv pipeline gnomad talkowski-lab written 7 weeks ago by cocchi.e8980
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Comment: C: Mutect2 somatic hemizygote variant on chrX
... Yes sorry Igor, I meant not really likely ...
written 8 weeks ago by cocchi.e8980
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Mutect2 somatic hemizygote variant on chrX
... I am working on calling some somatic variants from WES samples, I followed step-by-step the [GATK guidelines][1]. This is not a tumor sample so I don't compare the exome with another but with a multisaples [panel-of-normals][2]. Basically at the end of all filterings etc. you got a VCF file with `PA ...
gatk mutect2 chromosome-x hemizygosis somatic written 8 weeks ago by cocchi.e8980
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GATK mutect2 missing variant
... I have noticed a strange behavior of [GATK Mutect2][1], especially the variant `13-33329989-TGTCTC-T` is called if the BED file used in the command contains: 13 33329959 33330170 and is not called if another BED is used that contains: 13 33329974 33330100 but BOTH of them contain the `3 ...
gatk mutect2 mutation bed written 10 weeks ago by cocchi.e8980

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