Detect and visualize target mutations by scanning FastQ files directly - OpenGene/MutScan
Default: true -i : Input format [ vcf, bed ]. Default: VCF. -fileList : Input actually contains a list of files to process. -o : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF. -s , -stats : Name of stats file (summary). Attribute, mapping, and color information may be in separate files, i.e. in Attributes files, Mapping files, and Color files, or in a single Sample Information file. Script to convert GTC/BPM files to VCF. Contribute to Illumina/Gtctovcf development by creating an account on GitHub. Contribute to aromanel/Ethseq development by creating an account on GitHub. Pinpoints the mutation favored by selection. Contribute to alek0991/Isafe development by creating an account on GitHub.
VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerful tools: (1) SetOperator for performing… Structural variant detection and association testing - zeeev/wham vcf2introgress.py - Converts .vcf file to Introgress input files (4 files). Splits data into three categories: parental1, parental2 and admixed based on cluster assignment (provided in separate file; e.g. Contribute to statgenetics/rvnpl development by creating an account on GitHub. java -jar SOBDetector_v1.0.jar \ --input-type VCF \ --input-variants ./input-variants.vcf \ --input-bam ./input.bam \ --sample-name Sample1 --output-variants ./output.vcf \ --only-passed true Human haplotype-resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads - maiziex/Aquila_stLFR For single-sample assemblies, the command is RunTiledAssembly.sh. There is a helper script that will generate grid commands for SGE and Slurm in local_assembly/grid_scripts/ConfigureGridScripts.py:
A Python package for clustering of single nucleotide variants from high-through seqencing data. - fasterius/VarClust Download the VCF and the index (tbi) files from ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/Nistv3.3.1/GRCh38/. Then (assuming we are in the same directory as in the above example), enter the following command: Samtools allows two methods to do this: 1. By providing separate bam files for each sample, like this: samtools multi-sample variants: separate bam files samtools mpileup -uf hs37d5.fa \ NA12878.chrom20.Illumina.bwa.CEU.exome bam \ NA12891… Variant call format (VCF) files (Danecek et al. 2011) containing both homozygous and heterozygous variants from all samples should be used as input to the Combine Variants tool with the option “Combine variants and output site only if… Both the sequence letter and quality score are each encoded with a single Ascii character for brevity. Contribute to blachlylab/mucor development by creating an account on GitHub. Tool to conduct QC of single cell amplification. Contribute to abyzovlab/SSSelector development by creating an account on GitHub.
Multi-sample somatic variant caller. Contribute to IARCbioinfo/needlestack development by creating an account on GitHub. :mag_right: Detection and analysis of RNA editing evidence from VCF data - funkhou9/editTools This is not required in this example becasue the input VCF is phased. Generic germline variant annotation pipeline. Contribute to sigven/gvanno development by creating an account on GitHub. Partitions a VCF file using the four-gamete test. Contribute to tkchafin/FGTpartitioner development by creating an account on GitHub. Sample Preparation FAQ Download as pdf Complete Genomics Service FAQ Download as pdf CNV, SV, MEI FAQ Download as pdf Small Variants FAQ Download as pdf Managing Data FAQ Download as pdf Genome Voyager FAQ
The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing than 50% of samples have data"> ##FORMAT=
