<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37198?offset=120 https://bioinformaticsonline.com/bookmarks/view/28915/useful-bioinformatics-tools Mon, 29 Aug 2016 04:08:12 -0500 https://bioinformaticsonline.com/bookmarks/view/28915/useful-bioinformatics-tools <![CDATA[Useful Bioinformatics Tools]]> Collections of few handy tools for bioinformatician

http://molbiol-tools.ca/Convert.htm

Address of the bookmark: http://molbiol-tools.ca/Convert.htm

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/34699/biological-file-format-tutorial Sun, 17 Dec 2017 18:13:03 -0600 https://bioinformaticsonline.com/bookmarks/view/34699/biological-file-format-tutorial <![CDATA[Biological file format tutorial]]> This section explains some of the commonly used file formats in bioinformatics. The information provided here is basic and designed to help users to distinguish the difference between different formats. Please refer user manual or other information resources on web for more details.

  1. FASTA
  2. FASTQ
  3. SAM
  4. BAM
  5. VCF
  6. GFF
  7. GTF

Address of the bookmark: https://bioinformatics.uconn.edu/resources-and-events/tutorials/file-formats-tutorial/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43663/vcf2maf-convert Fri, 17 Dec 2021 03:20:01 -0600 https://bioinformaticsonline.com/bookmarks/view/43663/vcf2maf-convert <![CDATA[vcf2maf convert !]]> To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a Missense_Mutation close enough to a Splice_Site, can be labeled as either in MAF format, but not as both. This selection of a single effect per variant, is often subjective. And that's what this project attempts to standardize. The vcf2maf and maf2maf scripts leave most of that responsibility to Ensembl's VEP, but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the extensive support in parsing a wide range of crappy MAF-like or VCF-like formats we've seen out in the wild.

Address of the bookmark: https://github.com/mskcc/vcf2maf

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/43583/pango-lineage-analysis Mon, 15 Nov 2021 03:38:29 -0600 https://bioinformaticsonline.com/bookmarks/view/43583/pango-lineage-analysis <![CDATA[Pango Lineage Analysis !]]> The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

]]> Abhi