User: Luca Beltrame

gravatar for Luca Beltrame
Luca Beltrame170
Reputation:
170
Status:
Trusted
Location:
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
Last seen:
3 months, 2 weeks ago
Joined:
4 years ago
Email:
l************@marionegri.it

Posts by Luca Beltrame

<prev • 35 results • page 1 of 4 • next >
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Aggregate multiple VCFs into a single MAF or generate a multi-sample MAF from a multi-sample VCF
... **Note:** This is different from the many `vcf2maf` questions posted around Biostars. Like many others, I've been in need to generate a MAF file for use in downstream applications like `maftools` or `TRONCO`. My final goal is to obtain a multi-sample MAF file like the ones shipped by TCGA. Howev ...
maf file-formats conversion sequencing written 3 months ago by Luca Beltrame170
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Proper way to plot VCF files from structural variant callers
... Hello, I already made and annotated a number of VCF files with LUMPY and manta, and I'd like to find a way to properly view them: while I'm fine looking through them programmatically, it is useless for the biologists that will need to look at the data. Unfortunately, extensive Google searches haven ...
visualization circos sequencing written 18 months ago by Luca Beltrame170
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Comment: C: Targeted NGS: amplicon length vs read length
... We don't use the MiSeq software, everything is done off-instrument. ...
written 18 months ago by Luca Beltrame170
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Targeted NGS: amplicon length vs read length
... Hello, In our group we are about to design an amplicon-based targeted panel for NGS, and we're aiming at around 150 bp for mean amplicon sizes. The wet lab people came back to me asking to calculate the optimal number of samples to be loaded in the instrument (MiSeq). And this is where I have my qu ...
amplicon next-gen sequencing written 18 months ago by Luca Beltrame170 • updated 18 months ago by WouterDeCoster22k
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Comment: C: Quality Control Software For Targeted Sequencing?
... Looks interesting. Now all that's "left" is to find a way to convert Illumina's manifest format to Picard interval.... ...
written 3.8 years ago by Luca Beltrame170
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Quality Control Software For Targeted Sequencing?
... I'm mainly doing (amplicon-based) resequencing over small (50-100) number of genes with the Illumina technology. Aside from the normal metrics for quality control produced by Qualimap and FastQC, I'm wondering if there's something out there (aside TEQC, see below for while) that targets specifically ...
software ngs analysis sequencing written 3.8 years ago by Luca Beltrame170 • updated 3.8 years ago by brentp22k
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Comment: C: Build Phylogenetic Trees From Bam Files
... Thanks for the answer. I'm using retargeted sequencing on small number of targets (30 genes), so I'm assuming it won't be a big problem. When you mention a consensus sequence, you mean using stuff like pileup to generate it? ...
written 3.8 years ago by Luca Beltrame170
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Build Phylogenetic Trees From Bam Files
... Hello, more and more publications are showing phylogenetic trees (often rootless) to represent similarities between samples from the same origin (e.g. tumors). I've set out trying to do the same thing, except that all my searches didn't find anything, neither a way to do this directly, nor a way to ...
bam sequencing written 3.8 years ago by Luca Beltrame170 • updated 3.7 years ago by Fwip480
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Comment: C: Snp Calling Of Tcga Data Using Samtools
... You may want to look at the VT info field added by vcfsamplediff, which should have information on somatic/germline etc. ...
written 3.9 years ago by Luca Beltrame170
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Comment: C: Convert Cds-Based Coordinate To Genomic Coordinates
... More like genomic sequence (all the coordinates are mapped to the canonical variant of the gene), but yes, something like that. ...
written 3.9 years ago by Luca Beltrame170

Latest awards to Luca Beltrame

Popular Question 15 months ago, created a question with more than 1,000 views. For How To Interpret Dp Fields For Samples In Vcf Files?
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Handle Reads Ending With Deletions In Gatk?
Popular Question 17 months ago, created a question with more than 1,000 views. For Convert Cds-Based Coordinate To Genomic Coordinates
Great Question 3.5 years ago, created a question with more than 5,000 views. For Color Clustering Results Basing On Sample Classes In R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Represent Two Different Indels At The Same Position In A Multisample Vcf?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Re-Annotating An Existing Gff File?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Build Phylogenetic Trees From Bam Files
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Convert Cds-Based Coordinate To Genomic Coordinates
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Finding The Number Of Reads Which Support A Variant In Vcf
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Interpret Dp Fields For Samples In Vcf Files?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Targeted Sequencing - Calculating The Minimum Exon Coverage
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Sequencing Depth And Mutation Frequency
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Visualization Tools For Ngs Analysis Results, Suitable For Biologists
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Color Clustering Results Basing On Sample Classes In R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Loess Normalization And Scale Issues
Student 3.5 years ago, asked a question with at least 3 up-votes. For Color Clustering Results Basing On Sample Classes In R

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