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The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.
File conversion from VCF file is handled within the function call, followed by annotation and output to an Excel-compatible file. The script takes a number of parameters for annotation and outputs a VCF file with the annotations as key-value pairs inside of the INFO column of the VCF file for each genetic variant, e.g. "genomic_function=exonic".
jCard, "The JSON Format for vCard" is a standard proposal of 2014 in RFC 7095.RFC 7095 describes a lossless method of representing vCard instances in JSON, using arrays of sequence-dependent tag–value pairs. jCard has been incorporated into several other protocols, including RDAP, the Protocol to Access White Space Databases (PAWS, described in RFC 7545), and SIP, which (via RFC 8688) uses ...
Convert a bam file into a sam file. samtools view -bS sample.sam > sample.bam. Convert a sam file into a bam file. The -b option compresses or leaves compressed input data. samtools view sample_sorted.bam "chr1:10-13"
Additionally, the Bioconductor Biostrings package can be used to read and manipulate FASTA files in R. [25] Several online format converters exist to rapidly reformat multi-FASTA files to different formats (e.g. NEXUS, PHYLIP) for use with different phylogenetic programs, such as the converter available on phylogeny.fr. [26]
Import and export your personal data to a file for safekeeping. Personal data includes Mail, Favorites, Address Book, and settings. 1. Sign in to Desktop Gold. 2. Click the Settings icon. 3. While in the General settings, click the My Data tab. 4. Click Import or Export. 5. Select your file. 6. If exporting, create a password.
Avoid the stresses of hosting a holiday party by limiting guest beverage options so you can spend more time focusing on family and friends. Here are 5 tips to help.
BEDTools: program allowing the manipulation of coordinate sets and the extraction of sequences from a BED file. [6] BEDOPS: a suite of tools for fast boolean operations on BED files. [8] BedTk: a faster alternative to BEDTools for a limited and specialized sub-set of operations. [9] covtobed: a tool to convert a BAM file into a BED coverage ...