User: Ash

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Ash10
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1 year, 6 months ago
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Posts by Ash

<prev • 28 results • page 1 of 3 • next >
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Gene expression and chromatin state
... I want to compare the expression of a list of genes (mouse) in a specific organ e.g. lung. Also, the chromatin state e.g. which regions are repressed or transcriptionally active. I think MGI gene expression database for gene expression and ENCODE for chromatin? But I cannot figure out how to get ...
expression chromatin dna written 1 day ago by Ash10
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How many variant caller is needed for somatic mutations?
... Generally, can I safely use one variant caller e.g. Mutect2 if all my samples are normal matching? Because when 2 to 3 callers were used, the number of mutations decrease dramatically after intersecting the mutations. I am looking at the somatic mutations in normal tissues and the mutant clones can ...
snp variant caller written 4 days ago by Ash10
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Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
... What I understand is Tumor mutation burden (TMB) is `number of unique mutation in a sample`/ `the size of the capture` and variant allele fraction (VAF) is `tumour allele count` / `coverage` and can be infer as the size of the mutant clone. correct? Let say I am sequencing normal tissue to compare ...
maf tmb vaf written 4 days ago by Ash10
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bcftools isec: tandem mutations
... I am trying to use bcftools isec to find common variants between two callers. it mostly works find but when it is a tandem mutation e.g.CC>TT or GG>AA.. mutations instead of an SNP. It is not included in the intersect file? I have two vcf files that have five common tandem mutations. All five ...
isesc bcftools written 27 days ago by Ash10
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Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
... Thanks for the reply. But why do we have to isolate all rs IDs from the dbSNPs before using it to filter our sample vcf? ...
written 28 days ago by Ash10
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Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
... Hi WouterDeCoster, Just wondering why do we want to only filter the dbSNP variants with rs IDs? Correct me if I am wrong, I thought dbSNP accept submission of SNPs from disease and silence mutation SNPs. So will I be filtering some important disease-related SNPs? Thanks! ...
written 29 days ago by Ash10
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Filtering vcf with dbSNP
... Hi, From NCBI website, dbSNP accepts both disease or not SNPs [https://www.ncbi.nlm.nih.gov/books/NBK44447/#Content.what_classes_of_genetic_variatio][1]. I have some samples that do not have matching normals. I have done it with Mutect2 but want to use another caller to further verify my finding ...
filter bcftools dbsnp written 29 days ago by Ash10 • updated 10 days ago by Biostar ♦♦ 20
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Refseq file 0 coding length
... Hi, I would like to use gatk DepthOfCoverage to get coverage of each gene. I have created a refseq file according to gatk website from UCSC table browser. The first few lines of the refseq file are below but keep getting an error saying the coding length of some genes are 0. and the output gene cov ...
gatk depthofcoverage written 4 weeks ago by Ash10 • updated 4 weeks ago by lieven.sterck10k
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Comment: C: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
... Hi, this is the tool https://github.com/tsy19900929/snpeffToMaf ...
written 8 weeks ago by Ash10
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NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
... I have called variants with GRCm38 and annotated with snpeff with in built GRCm38.99.genome. When doing `snpefftomaf.pl` NCBI build column in the MAF file is 37? I checked the header of the VCF and confirmed it was GRCm38 that I used. Is there a way to check if the NCBI build was detected wrong o ...
maf genome ncbi build grcm38 reference written 8 weeks ago by Ash10

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Popular Question 10 months ago, created a question with more than 1,000 views. For Problem: GATK insallation

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