53 skills found · Page 1 of 2
broadinstitute / PicardA set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
pysam-developers / PysamPysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
knausb / VcfRTools to work with variant call format files
rutgerblom / SDDC.LabAutomate deployment and configuration of nested VMware Software-Defined Data Center environments including solutions like vSphere, vSAN, NSX, vSphere Kubernetes Service, Avi Load Balancer, Aria Operations for Logs, VCF 9, VyOS, and ISC BIND.
MRCIEU / GwasvcfReading, querying and writing GWAS summary data in VCF format
sigven / Vcf2tsvpyGenomic VCF to tab-separated values
opencb / Genome MapsAn open-source high-performance web-based HTML5 genome browser. Genome Maps can be customized and allow browsing user data such as BAM and VCF files among other formats.
biowdl / RNA SeqA BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
zhanxw / SeqminerQuery sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
dceoy / PdbioPandas-based Data Handler for VCF, BED, and SAM Files
griffithlab / VAtoolsA set of tools to annotate VCF files with expression and readcount data
biowdl / Germline DNAA BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
sauternic / VCard To CSVMakes vCard (.vcf) data readable
Gabaldonlab / JlohA tool to extract LOH blocks from VCF, BAM and FASTA data
ACAD-UofA / Guide To Manipulating PLINK EIG And VCF FilesA guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.
Zilong-Li / VcfppRThe fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049
smithijk / Vcf Fdw PostgresqlA PostgreSQL foreign data wrapper for VCF files.
HuntsmanCancerInstitute / USeq180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.
lifeomic / Spark VcfSpark VCF data source implementation for Dataframes
SouthGreenPlatform / VcfHunterVcfExplorer regroups several programs which principal aims are to map DNA and RNAseq data onto reference genome sequence, perform variant calling, manipulate vcf files, perform chromosome painting of accessions based on the contribution of ancestral groups, select marker for genetic map analysis and perform pairwise chromosome linkage of ordered markers.
