User: fabbri.marco

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Posts by fabbri.marco

<prev • 20 results • page 1 of 2 • next >
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Comment: C: VCF to maf
... My question was on possible alterative tools. ...
written 10 weeks ago by fabbri.marco0
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VCF to maf
... I need to convert a vcf file to maf file. I had problem to install vcf2maf on my old window machine (I am stuck at home for the virus). Any alternative? Maybe an R package. I need since I would like to use maftools. Thank for any suggestion. Best, Marco ...
vcf maf conversion written 10 weeks ago by fabbri.marco0
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Comment: C: Missing mappability file for mm10
... Thank you but I do not think I can use it for HMMcopy Marco ...
written 11 months ago by fabbri.marco0
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Missing mappability file for mm10
... I would like to use HMMcopy and ichorCNA for mm10. It looks there are no Mappability or Uniqueness of Reference Genome from ENCODE for mm10, so I can not generate the segmentation file. Anyone has already produced Mappability files for mm10 and wants to share? Any other suggestions? Thanks Marco ...
mm10 mappability written 11 months ago by fabbri.marco0
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Comment: A: Complete exon coordinate for ref seq gene
... In this RefSeq genome annotation file, for example for IL9R we have different exons in different transcripts, some are shared and some unique. I would like to have a single line per gene with the union of exon coordinates: results: IL9R chrX 155997580,156002905,156003448,156003676,15600441 ...
written 13 months ago by fabbri.marco0 • updated 13 months ago by genomax84k
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Complete exon coordinate for ref seq gene
... I have a list of ref-seq genes and I would like to get genome coordinates of all non-overlapping and non-replicated exons for each gene. I am designing a gene panel to detect mutations and I want to be sure to have all exons covered. Any suggestion, how to proceed? thank you Marco ...
exon ref-seq written 13 months ago by fabbri.marco0
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Canonical transcript exon bounderieis
... I have a list of HUGO symbols and would like to get the exon boundaries only of the canonical transcripts. thank you for suggestion ...
canonical exon written 14 months ago by fabbri.marco0
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varscan not taking opstions
... I am running varscan 2.4.3, mpileup2snp is not taking the settings as you can below, it works but with default settings any suggestion how to change them? varscan mpileup2snp sam1 –-min-coverage 10 –-min-var-freq 0.05 –-p-value 0.05 --output-vcf 1 > test6var005.vcf Only SNPs will be rep ...
mpileup2snp varscan2 setting written 2.1 years ago by fabbri.marco0 • updated 2.1 years ago by Pierre Lindenbaum128k
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varscan somatic without normal
... I am interested in somatic mutations using a gene panel ( focused on lymphoma). For a sample I do not have the normal counterpart. I would like to use varscan, any suggestion how to run the analysis? Thank you marco ...
varscan mutation written 2.1 years ago by fabbri.marco0
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Realignment disappeared in gatk4
... In GATK4 the indel realignment step will no longer be part of the pipeline. With my great surprise the tool has disappeared. My question, the algorithm is no more there because it doesn't improve the alignment? Do I need to search for a replace or should I just remove it from my pipeline since it is ...
gatk realignment written 2.2 years ago by fabbri.marco0 • updated 2.2 years ago by igor10k

Latest awards to fabbri.marco

Popular Question 9 months ago, created a question with more than 1,000 views. For nanopore-Illumina hybrid RNA assembly
Popular Question 21 months ago, created a question with more than 1,000 views. For Realignment disappeared in gatk4

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