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parseq/tsvc

By parseq

•Updated over 10 years ago

Image
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parseq/tsvc repository overview

⁠tsvc-4.4.3 image

Default command for this image is variant_caller_pipeline.py --help.

So, command to run image and to see help message from tvc-4.4.3:

docker run --rm parseq/tsvc:4.4.3

Or one can look at help message for tvcutils:

docker run -rm parseq/tsvc:4.4.3 tvcutils

To run TVC requires (see tvc-4.4.3 documentation⁠ for usage details):

  • reference file in fasta format
  • aligned bam file
  • tvc parameter file

optional input files:

  • bed file with target regions (region-bed)
  • bed file with amplicon coordinates for primer trimming (primer-trim-bed)
  • vcf file with hotspots data (hotspot-vcf)

It is possible to use tvcutils to prepare hotspots vcf files (see tvcutils prepare_hotspots documentation⁠ for usage details) or to validate target regions bed files (see tvcutils validate_bed documentation⁠).

NB:

  • directory with reference should contain index and should be writable
  • directory with reference should not contain file "dict"
  • directory with bam file should contain index

To use tvc from image the data volume or data volume container should be created.

Command to run tvc on example data (provided with tvc-4.4.3) and to save output into tmp directory on host machine:

    docker run --rm \
        -v ~/tmp:/mnt/tsvc-output parseq/tsvc:4.4.3 variant_caller_pipeline.py \
        --input-bam       /opt/tvc-4.4.3/share/TVC/examples/example1/test.bam \
        --reference-fasta /opt/tvc-4.4.3/share/TVC/examples/example1/reference.fasta \
        --region-bed      /opt/tvc-4.4.3/share/TVC/examples/example1/test_merged_plain.bed \
        --primer-trim-bed /opt/tvc-4.4.3/share/TVC/examples/example1/test_unmerged_detail.bed \
        --parameters-file /opt/tvc-4.4.3/share/TVC/pluginMedia/parameter_sets/ccp_somatic_lowstringency_pgm_parameters.json \
        --output-dir      /mnt/tsvc-output

Example of command to run tvc on user data and to save output into directory on the host machine:

docker run --rm \
    -v ~/directory/to/store/output:/mnt/tsvc-output \
    -v ~/directory/with/bam:/mnt/input_bam \
    -v ~/directory/with/reference:/mnt/reference \
    -v ~/directory/with/tsvc_parameters:/mnt/parameters \
    parseq/tsvc:4.4.3 variant_caller_pipeline.py\
    	--input-bam       /mnt/input_bam/filename.bam \
    	--reference-fasta /mnt/reference/reference.fasta \
    	--region-bed      /mnt/parameters/target_regions.bed \
    	--primer-trim-bed /mnt/parameters/panel.bed \
    	--parameters-file /mnt/parameters/parameters.json \
    	--output-dir      /mnt/tsvc-output

Example of command to run tvcutils validate_bed on user data and to store output on the host machine:

docker run --rm \
    -v ~/directory/to/store/output:/mnt/tsvc-output \
    -v ~/directory/with/reference:/mnt/reference \
    -v ~/directory/with/target_regions:/mnt/parameters \
    parseq/tsvc:4.4.3 tvcutils validate_bed \
        --reference /mnt/reference/reference.fasta \
        --target-regions-bed /mnt/parameters/designed.bed \
        --unmerged-detail-bed /mnt/tsvc-output/designed.unmerged-detail.bed \
        --merged-plain-bed /mnt/tsvc-output/designed.merged-plain.bed

Example of command to run tvcutils prepare_hotspots on user data and to store output on the host machine:

docker run --rm \
    -v ~/directory/to/store/output:/mnt/tsvc-output \
    -v ~/directory/with/reference:/mnt/reference \
    -v ~/directory/with/input_bed:/mnt/parameters \
    parseq/tsvc:4.4.3 tvcutils prepare_hotspots \
        --reference /mnt/reference/reference.fasta \
        --input-bed /mnt/parameters/hotspots.bed \
        --output-vcf /mnt/tsvc-output/hotspots.vcf

Tag summary

Content type

Image

Digest

Size

489 MB

Last updated

over 10 years ago

docker pull parseq/tsvc:4.4.3