User: Martina

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Martina30
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Posts by Martina

<prev • 18 results • page 1 of 2 • next >
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Answer: A: vcf2maf VEP annotated VCF conversion
... Oh.. Thank you very much :) ...
written 6 weeks ago by Martina30
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vcf2maf VEP annotated VCF conversion
... Dear all, I heard many times about possibility to convert annotated vcf to maf with vcf2maf by rewriting of name to *.vep.vcf (which marks that vcf is already annotated). But even when I do it, the vcf2maf program wants to annotate it again, which I don't want. Can you please advice me how to make i ...
vcf maf ngs vcf2maf wgs written 6 weeks ago by Martina30
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Comment: C: Running vcf2maf on snpeff-annotated vcfs
... I read about this possibility to just rewrite name of vcf to *.vep.vcf many times, but the program still wants to anotate the annotated vcf again. Have you got some idea why? $ vcf2maf.pl --input-vcf input.vep.vcf --output-maf output.vep.maf --vcf-tumor-id input_TUMOR --vcf-normal-id input_NORM ...
written 6 weeks ago by Martina30
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Literature for VCF filtering
... Hello, can you please advise me your favourite literature about variant calling, especially filtering? Some really good paper about which you think they have done it really precisely? Thank you very much! :) Martina ...
next-gen wes snp written 3 months ago by Martina30
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VCF quality indicators
... Dear colleagues, If you wanted to be sure that VCF from exome tumour-normal sequencing, focused on somatic variants you got from someone was done properly and you would believe BAM preparation and data quality, what would you check? I would go for: - in baits filter - QUAL filter - indels in homo ...
variant calling next-gen wes snp normal-tumor written 3 months ago by Martina30
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Answer: A: Variant calling: Sambama sort command not found
... Hello, I can highly recommend to use anaconda package manager. https://www.anaconda.com/distribution/ Check the virtual environment managing tutorial, its super easy and cool and practical. https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html ...
written 3 months ago by Martina30
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Repli-g single cell artefacts
... Dear colegues, I am struggling with SNP analysis of exome sequencing data of bulk DNA amplified by Repli-g single cell whole genome amplification kit, it looks like our data are full of artefacts. Healthy control (blood DNA) wasnt amplified. Do you guys have some advices about some pattern and type ...
sequencing wga next-gen snp repli-g single cell written 3 months ago by Martina30
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Bam QC, GC content
... Hello, I would like to ask you for advice with the assessment of BAM quality, especially QC content. This is the result of quality check by qualimap, exome sequencing with NEB and TWIST, only on-target regions are assessed. Have you got some idea why GC content is so shifted? It is a cancer sample, ...
next-gen written 8 months ago by Martina30
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function install.extras in R is not found
... Hello, I wanted to install and use NMF in R but I get an error: > Error in install.extras("NMF") : could not find function > "install.extras" Could you please advice me how to install install.extras to R? Thank you very much, Martina ...
R written 10 months ago by Martina30 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Amount of variants increased after bedtools subtract
... Hello Fin, thank you very much for your answer. Now I see that by default, bedtools filters out only variants with 100% overlap with bed file, so if I have a long variant covering 2 regions in bed file and I don't have -A option (which filters out variants with at least 1bp overlap), bedtools "touch ...
written 10 months ago by Martina30

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