User: cocchi.e89

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cocchi.e89120
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Posts by cocchi.e89

<prev • 106 results • page 1 of 11 • next >
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Comment: C: monozygotic twins ped file specification
... I tried but it makes absolutely no difference with the version without `.ped` file ...
written 11 weeks ago by cocchi.e89120
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monozygotic twins ped file specification
... Hi, I got some monozygotic twins samples (and a technical replicate of the same sample sequences twice) and I am running a `GATK GenotypeGVCFs` on their `GATK HplotypeCaller` called variants (through single `HaplotypeCaller` --> `GenomicsDBImport` data aggregation --> `GenotypeGVCFs` as per [G ...
gatk pedigree twin ped written 11 weeks ago by cocchi.e89120
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cwl GATK GenotypeGVCFs error in linux due to quotes in filenames
... Hi noticed that everytime I try to run `.cwl` scripts that include `GATK GenotypeGVCFs` the runner encounter an error that is related to how the previous step creates filenames in genomic DB (from `GATK GenomicsDBImport` called through `.cwl` too): > Invalid filename: '8$1$146364022' contains i ...
gatk cwl genotypegvcfs written 11 weeks ago by cocchi.e89120
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VEP repeated region flag
... Quick question, I googled around but found no answer for it, is there any VEP functionality that allows to know if a variant falls in a **repeated region**? (I am talking in order to screen for the PM4 ACMG criteria: *protein length changes as a result of in-frame deletions/insertions in a non-repe ...
vep variant human repeated-region written 3 months ago by cocchi.e89120 • updated 3 months ago by Emily_Ensembl21k
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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 4 months ago by cocchi.e89120
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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 months ago by cocchi.e89120 • updated 4 months 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 months ago by cocchi.e89120
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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 5 months ago by cocchi.e89120 • updated 5 months ago by newbio17320
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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 5 months ago by cocchi.e89120
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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 5 months ago by cocchi.e89120

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