User: cocchi.e89

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cocchi.e8990
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Posts by cocchi.e89

<prev • 101 results • page 2 of 11 • next >
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Error in GATK germline CNV caller
... I am trying to run GATK CNV germline on some human hg19 WGS samples. I followed the passages reported in their [best-practice guidelines][1]. I started with a 300 bp bin_length in ***PreProcessIntervals***. But after all passages if I try to extract values from a single sample with ***PostprocessGer ...
gatk cnv germline written 5 weeks ago by cocchi.e8990
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cwl: pass array of elements with repeated input flags
... I am trying to create a .cwl for the [GATK FilterIntervals][1] tool that takes several files as input, each one specified by `--input` flag. I know about cwl `itemSeparator` and here how I tried to pass the argument to the .cwl: - id: input_read_counts type: - "null" ...
array gatk cwl written 6 weeks ago by cocchi.e8990
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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 7 weeks ago by cocchi.e8990
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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 8 weeks ago by cocchi.e8990
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Comment: C: GATK Mutect2 Panel-Of-Normals generation
... Looks like it did the trick. Thank you very much @WouterDeCoster ! ...
written 11 weeks ago by cocchi.e8990
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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 12 weeks ago by cocchi.e8990
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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 12 weeks ago by cocchi.e8990 • updated 12 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 3 months ago by cocchi.e8990
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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 3 months ago by cocchi.e8990
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Comment: C: Mutect2 somatic hemizygote variant on chrX
... Yes sorry Igor, I meant not really likely ...
written 3 months ago by cocchi.e8990

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