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iontorrent/variantcaller

By iontorrent

•Updated over 9 years ago

ubuntu based image with ion-analysis and variant_caller_pipeline.py and the support files

Image
1

2.7K

iontorrent/variantcaller repository overview

Packages installed:

  • ion-analysis
  • ion-gpu (required by ion-analysis)

Variant Caller related files:

  • /usr/local/bin/variant_caller_pipeline.py
  • /usr/local/share/TVC/

Example from README on tvc_standalone⁠ page:

docker run --rm -t -v $(pwd):/output/ iontorrent/variantcaller variant_caller_pipeline.py \
--input-bam /usr/local/share/TVC/examples/example1/test.bam \
--reference-fasta /usr/local/share/TVC/examples/example1/reference.fasta \
--region-bed /usr/local/share/TVC/examples/example1/test_merged_plain.bed \
--primer-trim-bed /usr/local/share/TVC/examples/example1/test_unmerged_detail.bed \
--parameters-file /usr/local/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json \
--output-dir /output/tvc_example1

Tag summary

Content type

Image

Digest

Size

595.9 MB

Last updated

over 9 years ago

docker pull iontorrent/variantcaller