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Converting a VCF into a FASTA given some reference !
By Jit 2316 days agoconverting a VCF file into a FASTA file given a reference sequence
Converting BLAST output into CSV
Last updated 2537 days ago by Poonam MahapatraSuppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific...vcf2maf convert !
By Surabhi Chaudhary 1070 days agogithub.com - 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...VCF Compare !
By Rahul Nayak 1037 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...Tools for id conversion
By LEGE 551 days agobiit.cs.ut.ee - g:Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces. We provide at least 40 types of IDs for more than 60 species. The 98 different namespaces supported for human include Ensembl,...vcfR
By Archana Malhotra 3016 days agocran.r-project.org - Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in...-
Converting FASTQ to FASTA
Last updated 2505 days ago by NeelThere are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the... NCBI BLAST have added new columns to the Descriptions
By Neel 1451 days agoNCBI BLAST have added new columns to the Descriptions Table for web BLAST output.VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting,...
By Rahul Nayak 2298 days agovcftools.sourceforge.net - VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF...Pandoc: a universal document converter
By Surabhi Chaudhary 1247 days agohttps://pandoc.org/ - If you need to convert files from one markup format into another, pandoc is your swiss-army knife. Pandoc can convert almost all formats https://pandoc.org/index.html
