shanghungshih / Docker-for-NGS

This is docker for NGS

Docker-for-NGS

This is docker for NGS analysis https://hub.docker.com/u/adgh456/

• Notes: remember to mount your localPath to container and direct outputPath to specific mounted path of container!

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NGSMainWES

This contains human genome hg19 fasta, dbsnp138, COSMIC_v38 and some scripts.

1. genome coordinate：ucsc.hg19.fasta
2. dbSNP：dbsnp_138.hg19.vcf
3. COSMIC：CosmicAllMutsHeaderSorted.vcf
4. some scripts
5. seq_bed: agilent_region_OSCC_hg19_rmheader.bed (v2 only)
6. gnomad: gnomad.exomes.r2.0.2.sites.vcf.bgz (v3 only)

sudo docker pull adgh456/ngs-main:wes
sudo docker pull adgh456/ngs-main:wes_v2

• Usage:

sudo docker run --rm -v $localPath:/ref_data -i adgh456/ngs-main:wes_v2 mv /box_ref_data/* /box_scripts/* /ref_data

AfterQC

This is for pair-end NGS raw data auto-trimming and it'll output good, bad fastq and a html report. (using pypy to accelerate operation)

sudo docker pull adgh456/afterqc:afterqc_pypy2

• Usage:

sudo docker run --rm -v $localPath:/AfterQC/data -i adgh456/afterqc:afterqc_pypy2 pypy after.py -h

Bwa

This is for fasta indexing, fastq data alignment and generate sam file.

sudo docker pull adgh456/bwa:0.7.15

• Usage:

sudo docker run --rm -v $localPath:/data -i adgh456/bwa:0.7.15 bwa --help

Samtools

This is for building index for fasta, sam, bam...

sudo docker pull adgh456/samtools:1.3.1
# or
sudo docker pull adgh456/samtools:0.1.19

• Usage:

sudo docker run --rm -v $localPath:/data -i adgh456/samtools:1.3.1 samtools --help

Picard

This is for building fasta dict.

sudo docker pull adgh456/picard:2.9.0-1-gf5b9f50-SNAPSHOT

• Usage:

sudo docker run --rm -v $localPath:/data -i adgh456/picard:2.9.0-1-gf5b9f50-SNAPSHOT java -jar picard.jar --help

GATK3

gatk-v3.8-registered image was already registered. No need to register everytime.

sudo docker pull adgh456/gatk:gatk-v3.8-registered

• Usage:

sudo docker run --rm -v $localPath:/data -i adgh456/gatk:gatk-v3.8-registered gatk --help

GATK4

sudo docker pull broadinstitute/gatk:4.0.4.0

• Usage:

sudo docker run --rm -v $localPath:/gatk/data -i broadinstitute/gatk:4.0.4.0 gatk --help

GATK for CNV

This is for copy number variant detection.

sudo docker pull adgh456/gatk:1.0.0.0-alpha1.2.3

• Usage:

sudo docker run --rm -v $localPath:/gatk-protected-1.0.0.0-alpha1.2.3/data -i adgh456/gatk:1.0.0.0-alpha1.2.3 java -jar /gatk-protected-1.0.0.0-alpha1.2.3/build/libs/gatk-protected.jar --help

MSIsensor

This is for Microsatellite Instability detection.

sudo docker pull adgh456/msisensor:0.2

• Usage:

sudo docker run --rm -v $localPath:/data -i adgh456/msisensor:0.2 msisensor --help

Breakmer

This is for Structural variants detection.

sudo docker pull adgh456/breakmer:v0.0.2

Meerkat

This is for Structural variants detection.

sudo docker pull adgh456/meerkat:v0.189

Phial

This is for FDA-approved drug annotation and visualization (input: maf.txt from Oncotator).

sudo docker pull adgh456/phial:v1.0

NCBI-edirect

This is for access NCBI API (ex. get NM).

sudo docker pull adgh456/edirect

NCBI-remap

This is for NCBI coordinates remap.

sudo docker pull adgh456/tools:ncbi-remap

bam-reheader

This is for bam reheader.

sudo docker pull adgh456/tools:bam-reheader