You can subset alignment files with samtools on the command line, e. Samtools supports streaming files and piping commands together both using local and remote files. You can get more help with samtools from the samtools help mailing list. Our filename conventions depend on the data format being named. This is described in more detail below. Our sequence files are distributed in gzipped fastq format.
Our files are named with the SRA run accession E? All the reads in the file also hold this name. If there is also a file with no number it is name this represents the fragments where the other end failed qc. Our variant files are distributed in vcf format , a format initially designed for the Genomes Project which has seen wider community adoption.
This name starts with the population that the variants were discovered in, if ALL is specifed it means all the individuals available at that date were used. Then the region covered by the call set, this can be a chromosome, wgs which means the file contains at least all the autosomes or wex this represents the whole exome and a description of how the call set was produced or who produced it, the date matches the sequence and alignment freezes used to generate the variant call set.
Next a field which describes what type of variant the file contains, then the analysis group used to generate the variant calls, this should be low coverage, exome or integrated and finally we have either sites or genotypes. A sites file just contains the first eight columns of the vcf format and the genotypes files contain individual genotype data as well. Release directories should also contain panel files which also describe what individuals the variants have genotypes for and what populations those individuals are from.
The Phase 1 integrated variant set does not report the depth of coverage for each individual at each site. We instead report genotype likelihoods and dosage. If you would like to see depth of coverage numbers you will need to calculate them directly.
The bedtools suite provides a method to do this. These commands also require samtools , tabix and vcftools to be installed. This command gives you a bedgraph file of the coverage of the HG bam between ,,,, This command gives you the vcf file for ,,,, with just the genotypes for HG You can find more information about bed file formats please see the Ensembl File Formats Help.
For more information you may wish to look at our documentation about data slicing. Our data portal has a page for each sample. At the bottom of the page, the various data collections that the sample is present in are listed in tabs. Each tab then lists the available files for that sample, including seqeunce data, genotype arrays, alignments and VCFs.
An example is the page for NA Sample IDs can be entered in the search box to locate a given sample. To understand the data available for larger groups of samples, the samples and population tabs of the portal can be used to explore available data.
Before that, you need to understand more about the vCard file format. If you have multiple email contacts in vCard file format or. Therefore, to process how to combine these several vCard data files into a single file, you can take the help of the vCard Merge Software. It can quickly and efficiently merge vCard files into a VCF.
Download Now Purchase Now. You can edit your Q and add all the details. Add a comment. Active Oldest Votes. File formats examples: sample1 1 sample2 2 sample3 2 or sample1 M sample2 F sample3 F or a. Improve this answer. Michael Hall Michael Hall 2 2 silver badges 10 10 bronze badges. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown. Featured on Meta. Reducing the weight of our footer.
Note: A fast htslib C version of this tool is now available see bcftools annotate. Requires tabix indexed file with annotations. Usage: cat in. The dash in this example indicates that the third column should be ignored. The descriptions can be read from a file, one annotation per line. If argument to -f is a file, user-defined filters be applied. See User Defined Filters below. Edit and run with -f filters. The examples below are self-explanatory.
The script also computes numbers such as nonreference discordance rates including multiallelic sites , compares actual sequence useful when comparing indels , etc. Note: A fast htslib C version of this tool is now available see bcftools stats.
Concatenates VCF files for example split by chromosome. Note that the input and output VCFs will have the same number of columns, the script does not merge VCFs by position see also vcf-merge.
In the basic mode it does not do anything fancy except for a sanity check that all files have the same columns. When run with the -s option, it will perform a partial merge sort, looking at limited number of open files simultaneously. A tool for finding differences between groups of samples, useful in trio analysises, cancer genomes etc.
Only novel alleles are reported -n. Finally the sites are sorted by confidence of the site being different in the child -k5,5nr. Please take a look at vcf-annotate and bcftools view which does what you are looking for. Apologies for the non-intuitive naming. Note: A fast HTSlib C version of a filtering tool is now available see bcftools filter and bcftools view.
Read more About: Currently calculates in-frame ratio. Given multiple VCF files, it can output the list of positions which are shared by at least N files, at most N files, exactly N files, etc.
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