User: Max Ivon

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Max Ivon120
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Russian Federation
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Posts by Max Ivon

<prev • 42 results • page 1 of 5 • next >
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Combine several VCF files
... I've performed variant calling with two callers. One calls haplotypes and other calls mutations as single variants. As a result I have two VCF files where sometimes identical variants are written in different forms. For example: One file: chr1 61987 . AAG GAC Another file: ...
vcf bcftools written 9 months ago by Max Ivon120 • updated 9 months ago by Brice Sarver3.5k
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Comment: C: Detecting Structural variants in sequencing data
... What type of SVs you are interested in? Copy number variation or rearrangements or both? Germline or somatic? If you have non BWA aligned BAM files you can realign data with BAM and use LumpySV if you are sure in its performance for your data. ...
written 2.7 years ago by Max Ivon120
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Comment: C: Reference and mutant allele of a SNP rsID
... For this goal you may download VCF files from dbSNP ftp server and surf them for each rsID you need. For example here ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/ will be files you need **for hg38 genome build**. Nevertheless it may require sufficient computational resources an ...
written 2.8 years ago by Max Ivon120
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Answer: A: Reference and mutant allele of a SNP rsID
... You may go directly to dbSNP and check it there https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=80357307 Here "RefSNP Alleles" lists all observed alleles associated with this rsId (keep in mind strand - reverse or forward) Ancestral Allele is listed below as well as contig allele (reference ...
written 2.8 years ago by Max Ivon120
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Comment: C: how to get exact break point in COSMIC fusion gene?
... The problem is that COSMIC arrange data from different sources and exact breakpoints are not always known just becaase the source experiment employed rna-seq - genome break point just can be grasped in this case. If you want to determine the spectrum of breakpoints of ALK fusions I would recommend y ...
written 2.8 years ago by Max Ivon120
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Comment: C: Multiple biopsy issue in MutSig and GISTIC tools
... There are several issues with merging data from different biopsies. When we talk about biopsies taken at the same time point the major is tumor inter- and intra- heterogeneity. When we talk about different time point it is tumor evolution - for example, molecular landscape of metastatic castrate-res ...
written 2.8 years ago by Max Ivon120
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Answer: A: Database for Somatic Copy Numbers
... If you want to focus on high confidence mutations you may want to have a look at results of the systemic studies like TCGA or ICGC rather than just mutation database. Try cbioportal.org to overview such projects for different tumor types and focus on the one you are interested in. If you dont need t ...
written 2.8 years ago by Max Ivon120
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Removing fused transcripts from RNA seq data
... Hello! I have performed alignment of paired-end data with tophat with the following options: tophat --no-coverage-search --max-multihits 1 -p 4 -o <...> <...> <...> -G <...> What would be the easiest way to remove read pairs coming from fused transcripts based on annot ...
rna-seq written 3.2 years ago by Max Ivon120
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Comment: C: Bowtie2-Samtools. Too many degenerate bases
... There is a bug with several version of samtools (dont know which exactly). It results in improper mpileup (reference is not recognised properly and all or major part is substituted with N). Dont know why it helps, so im not sure wether it will help you or no - may be you faced another error, but it ...
written 4.4 years ago by Max Ivon120
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Comment: C: How does OMIM select the clinically associated variants (SNPs)?
... Yes, OMIM is manually curated (http://www.omim.org/help/faq). Another sources of pathogenic mutations are CLINVAR and HGMD, which are basically also manually curated, but generally contain more mutations (and more false positive ones, keep this in mind). So OMIM does not hide any variants and show e ...
written 4.4 years ago by Max Ivon120

Latest awards to Max Ivon

Popular Question 18 months ago, created a question with more than 1,000 views. For Illumina BaseSpace File System
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Illumina BaseSpace File System
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Clinical utilization of NGS data in cancer research
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Clinical utilization of NGS data in cancer research
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Human Exome GC content
Popular Question 2.7 years ago, created a question with more than 1,000 views. For PGM reads 3' end trimming
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Identifying mutations from Paired-End Sequencing data
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Human Exome GC content
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Human Exome GC content
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Can'T Find Indels With Samtools (Onyly Get Snps)
Student 4.4 years ago, asked a question with at least 3 up-votes. For NGS hybrid reads
Scholar 5.2 years ago, created an answer that has been accepted. For A: GATK dbSNP for Ensembl

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