Results for "vcf"
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Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...ner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing.../glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vcf.gz \ -s AAATGTAAACATTTT...1580 days ago
Nucleus: Python and C++ code for reading and writing genomics data.
Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables p...1575 days ago
- List of publically available databases on google server. More at https://software.broadinstitute.org/gatk/download/bundle ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/. ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/
1564 days ago
FiNGS: Filters for Next Generation Sequencing
...ple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into exi...1184 days ago
- To convert a VCF into a MAF, each variant must be mapped to only on...t's what this project attempts to standardize. The vcf2maf and maf2maf scripts leave...e their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the mo...
891 days ago
- compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagsta...
857 days ago
CrossMap: program for genome coordinates conversion between different assemblies
...ts commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.851 days ago
Minda: a tool for evaluating structural variant (SV) callers
Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set created from multiple VCF input files.56 days ago
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