User: cocchi.e89

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cocchi.e89110
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Posts by cocchi.e89

<prev • 102 results • page 1 of 11 • next >
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GATK somatic CNV results
... I am using [GATK somatic-CNV pipeline][1] for some hg38 human sample (normal-tumor matched). In CollectAllelicCounts interval_list ([here][2] and [here][3] the discussions) I have tried to use both: 1. gnomad genomes AF>0.02 sites ([plot link][4]) ![gnomad genomes AF>0.02 PlotModeledSegme ...
gatk cnv somatic written 12 days ago by cocchi.e89110
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VEP - gnomAD v3 (hg38) annotation AF
... I am working with some WGS human hg38 tests. I noticed that VEP has as default [only gnomAD exomes][1] included, and adding the annotation through [dbNSFP][2] only works for SNP (and not INDEL). I wondered if there is there a way to manually add AF annotation directly from [gnomAD database files][ ...
vep hg38 gnomad annotation written 5 weeks ago by cocchi.e89110 • updated 18 days ago by Biostar ♦♦ 20
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CNV .vcf retrieve involved genes
... I have some CNV .vcf files generated through [GATK Germline CNV pipeline][1], and I'd like to get the genes involved in each CNV. Here an example of the VCF file: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A13665 chr1 821001 CNV_chr1_821001_1632000 N . 3076.53 . END=1632000 GT:CN:NP:QA: ...
vcf gatk genes cnv written 5 weeks ago by cocchi.e89110
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convert GATK germline CNV .vcf output to .seg/.cns format to plot
... I have some CNV calls operated through [GATK germline CNV pipeline][1], the output of such pipeline is a ***.vcf*** file (*.segments.vcf.gz*) that looks like this: zgrep -v "^#" /home/ec3408/germlineCNV/A13661_PostGermlineCNVCaller/A13661.segments.vcf.gz | head chr1 821001 CNV_chr1_821001_ ...
vcf gatk seg cnv cns written 6 weeks ago by cocchi.e89110 • updated 6 weeks ago by newbio17240
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Comment: C: all coding regions .bed file hg38 Whole Genome Sequencing
... I did and de-piped command, mine was more a theoretical question ...
written 7 weeks ago by cocchi.e89110
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Comment: C: all coding regions .bed file hg38 Whole Genome Sequencing
... thanks so much, I was wondering, what are the regions that are filtered out between line 2 and line 3? (regions that are flagged as *protein_coding* but not *exons*? ...
written 7 weeks ago by cocchi.e89110
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all coding regions .bed file hg38 Whole Genome Sequencing
... Quick question: is there out there a .bed (or similar) files that span over all coding regions in hg38 coordinates? I need to analyze some WGS samples Thank you very much in advance for any help! ...
wgs coding bed written 7 weeks ago by cocchi.e89110 • updated 7 weeks ago by Pierre Lindenbaum131k
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comparison of variants between WGS samples
... I never worked on such specific task so there may be a simple solution that I don't know, I need to find the rate of similarity and find out what are the differences between 2 WGS human samples. Let's say I want to know what variants are specific of *sample1*, what are specific of *sample2* and what ...
wgs gatk differences human variants written 7 weeks ago by cocchi.e89110 • updated 7 weeks ago by harold.smith.tarheel4.6k
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GATK Mutect2 tumor mode
... I am working on some human WGS tumor samples and I want to call somatic variants against the normal tissue sample. I see that Mutect2 had a tumor-mode in [previous Mutect2 (now deprecated) guidelines][1] but I can not find it anymore in [current GATK Mutect2 guidelines][2] where only PoN are used. ...
wgs tumor mutect2 human gatk written 7 weeks ago by cocchi.e89110
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GATK CNV germline plot vcf results
... I am working on some CNV analysis in human WGS samples through [GATK CNV germline pipeline][1]. I was wondering if there is any easy method to plot these results (I know they integrated it in the [somatic CNV pipeline][2]). Here an example of the results *.vcf*: #CHROM POS ID REF ALT QUAL FILT ...
vcf gatk germline cnv plot written 9 weeks ago by cocchi.e89110

Latest awards to cocchi.e89

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Popular Question 4 months ago, created a question with more than 1,000 views. For gnomaAD exome and genome AF differences
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