micro-read Copy Number Variant Regions finder
738
mrCaNaVaR analyzes the mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.
Code and full README available at https://github.com/BilkentCompGen/mrcanavar
Auto mode assumes the mrsFAST .index file is also available in the input directory. Docker image assumes that the /input port is also writable.
Sample command lines for the mrcanavar-auto mode:
Different input/output directories:
docker run --user=$UID -v ${PWD}:/input -v ${PWD}:/output alkanlab/mrcanavar mrcanavar-auto --ref /input/human_g1k_v37_masked.fasta --conf /input/human_g1k_v37.cnvr --input /input/file1.fastq.gz,/input/file2.fastq.gz,/input/file3.fastq.gz --gene /input/b37_genes.bed --threads 4 --mem 16
Same input/output:
docker run --user=$UID -v ${PWD}:/mrcanavar alkanlab/mrcanavar mrcanavar-auto --ref human_g1k_v37_masked.fasta --conf human_g1k_v37.cnvr --input file1.fastq.gz,file2.fastq.gz,file3.fastq.gz --gene b37_genes.bed --threads 4 --mem 16
Same input/output directories, BAM or CRAM input (single file only):
docker run --user=$UID -v ${PWD}:/mrcanavar alkanlab/mrcanavar mrcanavar-auto --ref human_g1k_v37_masked.fasta --unmasked-ref human_g1k_v37.fasta --conf /human_g1k_v37.cnvr --aln-input file1.cram --gene b37_genes.bed --threads 4 --mem 16
Same input/output directories, BAM or CRAM input (single file only), skip generating SAM(.gz) files:
docker run --user=$UID -v ${PWD}:/mrcanavar alkanlab/mrcanavar mrcanavar-auto --ref human_g1k_v37_masked.fasta --unmasked-ref human_g1k_v37.fasta --conf /human_g1k_v37.cnvr --aln-input file1.cram --gene b37_genes.bed --threads 4 --mem 16 --no-sam
Content type
Image
Digest
Size
147 MB
Last updated
over 7 years ago
docker pull alkanlab/mrcanavar