https://divingintogeneticsandgenomics.com/tags/vcf/ Recent content in VCF on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Tue, 25 Aug 2015 13:36:00 -0700 https://divingintogeneticsandgenomics.com/archive/sort-with-header-maintained/ Tue, 25 Aug 2015 13:36:00 -0700 https://divingintogeneticsandgenomics.com/archive/sort-with-header-maintained/ We usually want to maintain header when we do something for the body of the text. You can find a body function here which can only accept streams and assumes only one line header. Use subshells and awk can do the same job and potentially more flexible. View this gist on GitHub The original credits go to Aaron Quinlan. see a gist below to sort vcf files in natural chromosome order :chr1 chr2 chr3. https://divingintogeneticsandgenomics.com/archive/vcf-file-annotation-and-manipulation-tools/ Sat, 29 Jun 2013 05:14:00 -0700 https://divingintogeneticsandgenomics.com/archive/vcf-file-annotation-and-manipulation-tools/ VCF (variant calling format) file, as specified in 1000 Genome http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 is a common file to handle the variant information from the NGS sequencing data. many tools have been developed to manipulate, extract information with this format. some popular ones are: tabix http://samtools.sourceforge.net/tabix.shtml for fast indexing and extracting certain regions of the whole genome. VCFtools http://vcftools.sourceforge.net/ for many more manipulations including annotating, merging, concatenating, comparing etc. bedtools http://code.google.com/p/bedtools/ for genomic region overlapping calculation. https://divingintogeneticsandgenomics.com/archive/use-tabix-to-extract-subset-of-sam-bed-and-vcf-files/ Fri, 17 May 2013 11:14:00 -0700 https://divingintogeneticsandgenomics.com/archive/use-tabix-to-extract-subset-of-sam-bed-and-vcf-files/ see here: http://davetang.org/muse/2013/02/22/using-tabix/ and here : http://www.biostars.org/p/43609/ and here: http://www.1000genomes.org/category/tabix disclaimer: credits go to the original authors, refer to the links above for detailed information. You can use tabix to extract subsets of the vcf files from the 1000genomes websites. Thanks to the fact that tabix uses a index file, you will be able to download only portions of the files, without having to download everything in local. Example: