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        "author": "Welliton Souza",
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        "description": "# An automated tool for processing whole-exome sequencing data\n\nWhole-exome sequencing has been widely used in clinical applications for the identification of the genetic causes of several diseases.\n_HPexome_ automates many data processing tasks for exome-sequencing data analysis of large-scale cohorts.\nGiven ready-analysis alignment files it is capable of breaking input data into small genomic regions to efficiently process in parallel on cluster-computing environments.\nIt relies on Queue workflow execution engine and GATK variant calling tool and its best practices to output high-confident unified variant calling file.\nOur workflow is shipped as Python command line tool making it easy to install and use. \n\nRequirements\n\n- BAM files must be sorted in `coordinate` mode. See [sort bam files](https://github.com/labbcb/hpexome/blob/master/docs/sort_bam_files.sh) script.\n- BAM files must have `@RG` tags with `ID, SM, LB, PL and PU` information. See [fix rg tag](https://github.com/labbcb/hpexome/blob/master/docs/fix_rg_tag_bam.sh) script.\n\n## Example\n\nThe following command line takes a list of ready-analysis BAM files stored in `alignment_files` directory and reference genomes files (version b37).\nThen it breaks input data into smaller parts (`--scatter_count 16`) and submits to SGE batch system (`--job_runner PbsEngine`).\nAll samples will be merged into a single VCF files (`--unified_vcf`) and output files will be written in `result_files` directory.\n\n```bash\nhpexome \\\n    --bam alignment_files \\\n    --genome references/b37/human_g1k_v37_decoy.fasta  \\\n    --dbsnp references/b37/dbsnp_138.b37.vcf \\\n    --indels references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf \\\n    --indels references/b37/1000G_phase1.indels.b37.vcf \\\n    --sites references/b37/1000G_phase1.snps.high_confidence.b37.vcf \\\n    --sites references/b37/1000G_omni2.5.b37.vcf \\\n    --unified_vcf \\\n    --scatter_count 16 \\\n    --job_runner GridEngine \\\n    result_fies\n```\n\nFor more information see <http://bcblab.org/hpexome>.\n\n\n",
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        "name": "HPexome",
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