gatk4-genome-processing-pipeline-azure
sv-callers
| gatk4-genome-processing-pipeline-azure | sv-callers | |
|---|---|---|
| 4 | 1 | |
| 7 | 71 | |
| - | - | |
| 0.0 | 2.9 | |
| 2 months ago | 3 months ago | |
| wdl | Python | |
| BSD 3-clause "New" or "Revised" License | Apache License 2.0 |
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gatk4-genome-processing-pipeline-azure
- What are some good examples of well-engineered bioinformatics pipelines?
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Do you know how to get CNVs out of WES data sorted.bam files? (Free)
The GATK suite is pretty standard for calling germline mutations. Somatic mutation calling is a lot newer/trickier, so I'm just going to link to the GDC's practices.
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Best way to document tool?
This pre-processing pipeline from Microsoft (adapted from the Broad Institute/GATK) is pretty well-documented - at least in my opinion - with input requirements, expected outputs, software requirements, etc.
sv-callers
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Do you know how to get CNVs out of WES data sorted.bam files? (Free)
Generally, you have multiple ways to tackle this kind of a problem. For short read sequencing you have two types of CNV detection - readdepth based and paired-end based. CNVpytor (CNVnator) for example, is the former. You also have manta and lumpy. A lot of good pipelines use more than one SV caller and integrate them. For example: https://github.com/GooglingTheCancerGenome/sv-callers
What are some alternatives?
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
sage - Proteomics search & quantification so fast that it feels like magic
covalent - Pythonic tool for orchestrating machine-learning/high performance/quantum-computing workflows in heterogeneous compute environments.
veba - A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
zarp - The Zavolab Automated RNA-seq Pipeline
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data