mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
...bout 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a B...1632 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype str...1599 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list...1560 days ago
1560 days ago
Best Practices for Variant Calling with the GATK
...d Roazen PDF Video 03/19/15 Introduction to variant discovery: calling cohorts Louis Bergelson PDF Video 03/19/15 Variant calling and joint genotyping Sheila...1535 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
...h known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs ag...1448 days ago
URMAP, an ultra-fast read mapper
...ithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage...1284 days ago
QuasiModo - Quasispecies Metric Determination on Omics
...sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar data...1044 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency...1044 days ago