genome/qc-metric-aggregator genome/qc-metric-aggregator

  • Stars
    star
    1
  • Language
    Python
  • License
    MIT License
  • Created over 4 years ago
  • Updated about 3 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
genome/qc-metric-aggregator
github

genome

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

More Repositories

1

bam-readcount

Count bases in BAM/CRAM files
CMake
300
star
2

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
C++
160
star
3

sciclone

An R package for inferring the subclonal architecture of tumors
R
115
star
4

breakdancer

SV detection from paired end reads mapping
C++
110
star
5

analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.
Common Workflow Language
102
star
6

gms

The Genome Modeling System installer
Perl
77
star
7

genome

Core modules used by the GMS
Perl
61
star
8

bfx-workshop

A course on genomics and bioinformatics from WU
HTML
55
star
9

somatic-sniper

A tool to call somatic single nucleotide variants.
C
40
star
10

docs

22
star
11

joinx

a tool for processing .bed and .vcf files
C++
21
star
12

scrna_mutations

Supplementary data for Petti, et al 2019 scRNA mutation publication
Python
16
star
13

mendelscan

Analyze exome data for Mendelian disorders. Still in alpha-testing.
Java
10
star
14

ptero

Shell
9
star
15

tigra-sv

8
star
16

sciclone-meta

accessory scripts and documentation related to the sciclone R package at genome/sciclone
R
6
star
17

rss2jira

Create JIRA issues when keywords are matched in RSS feeds.
Python
5
star
18

docker-rnaseq

A fat docker image for running RnaSeq
R
4
star
19

UR

Rich Transactional Objects for Perl
Perl
4
star
20

bmm

R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions
R
4
star
21

dindel-tgi

A fork of dindel
C++
3
star
22

docker-bcftools

Docker container for bcftools
Dockerfile
3
star
23

vcf-evaluation

scripts and modules to facilitate comparing gold standard VCFs
Perl
3
star
24

docker-star

Docker container for the star aligner
Dockerfile
3
star
25

docker-bam_readcount_helper-cwl

Python
3
star
26

graphite

Graphite Config and Cron Scripts
Perl 6
3
star
27

ptero-lsf

Ptero services to run commands via LSF
Python
2
star
28

cle-chromoseq

Repository for CLE ChromoSeq Assay
Python
2
star
29

pairoscope

simple static plots of read pairing information
C++
2
star
30

docker-dna-alignment

A fat docker image for running alignment
Shell
2
star
31

aml31Benchmarking

R
2
star
32

cle-myeloseqhd

Python
2
star
33

tgi-workflow

the workflow server used at TGI
Perl
2
star
34

flow-core

JavaScript
2
star
35

cncwl

1
star
36

docker-vep-cwl

Variant of vep image without an ENTRYPOINT
1
star
37

cle-myeloseq

Repo for cle myeloseq/haloplex assay
Perl
1
star
38

docker-gossamer

Docker container for gossamer bioinformatics suite
1
star
39

ptero-workflow

Client-facing API for the PTero system
Python
1
star
40

cle

Repo for cle related software
WDL
1
star
41

docker-custom-clinvar-vcf

Python
1
star
42

docker-samtools-cwl

Dockerfile
1
star
43

ptero-petri

Petri net core of the PTero system
Python
1
star
44

somatic-snv-test-data

Example Data for SomaticSniper
1
star
45

build-common

common build scripts used in c/c++ projects
Python
1
star
46

nessy-client-perl

Perl client for the nessy-server lock daemon
Perl
1
star
47

nessy-server

Python
1
star
48

cancer-genomics-workflow-wiki

A full featured, including pull requests, git repo for the arvados_trial Wiki
Shell
1
star
49

docker-fgbio

A docker image for using fgbio
1
star
50

docker-strelka

A docker image for Strelka
1
star