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GitHub / ccmbioinfo / crg2

Research pipeline for exploring clinically relevant genomic variants

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ccmbioinfo%2Fcrg2

Stars: 16
Forks: 5
Open Issues: 46

License: apache-2.0
Language: Python
Repo Size: 4.48 MB
Dependencies: 167

Created: about 4 years ago
Updated: 19 days ago
Last pushed: 19 days ago
Last synced: 19 days ago

Files
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    Dependencies
    wrappers/EH/environment.yaml conda
    wrappers/EHdn/environment.yaml conda
    wrappers/bcftools/annotate/environment.yaml conda
    wrappers/bcftools/call/environment.yaml conda
    wrappers/bcftools/concat/environment.yaml conda
    wrappers/bcftools/filter/environment.yaml conda
    wrappers/bcftools/index/environment.yaml conda
    wrappers/bcftools/isec/environment.yaml conda
    wrappers/bcftools/merge/environment.yaml conda
    wrappers/bcftools/norm/environment.yaml conda
    wrappers/bcftools/reheader/environment.yaml conda
    wrappers/qualimap/environment.yaml conda
    wrappers/bcftools/stats/environment.yaml conda
    wrappers/bcftools/view/environment.yaml conda
    wrappers/bedtools/bamtofastq/environment.yaml conda
    wrappers/bedtools/coveragebed/environment.yaml conda
    wrappers/bedtools/intersect/environment.yaml conda
    wrappers/bedtools/merge/environment.yaml conda
    wrappers/bedtools/slop/environment.yaml conda
    wrappers/bwa/aln/environment.yaml conda
    wrappers/bwa/index/environment.yaml conda
    wrappers/bwa/mem/environment.yaml conda
    wrappers/bwa/mem-samblaster/environment.yaml conda
    wrappers/bwa/sampe/environment.yaml conda
    wrappers/bwa/samse/environment.yaml conda
    wrappers/fastq_screen/environment.yaml conda
    wrappers/fastqc/environment.yaml conda
    wrappers/freebayes/environment.yaml conda
    wrappers/gatk/baserecalibrator/environment.yaml conda
    wrappers/gatk/combinegvcfs/environment.yaml conda
    wrappers/gatk/genotypegvcfs/environment.yaml conda
    wrappers/gatk/haplotypecaller/environment.yaml conda
    wrappers/gatk/mutect/environment.yaml conda
    wrappers/gatk/selectvariants/environment.yaml conda
    wrappers/gatk/splitncigarreads/environment.yaml conda
    wrappers/gatk/variantfiltration/environment.yaml conda
    wrappers/gatk/variantrecalibrator/environment.yaml conda
    wrappers/gatk3/baserecalibrator/environment.yaml conda
    wrappers/gatk3/haplotypecaller/environment.yaml conda
    wrappers/gatk3/indelrealigner/environment.yaml conda
    wrappers/gatk3/printreads/environment.yaml conda
    wrappers/gatk3/realignertargetcreator/environment.yaml conda
    wrappers/igv-reports/environment.yaml conda
    wrappers/manta/environment.yaml conda
    wrappers/metasv/environment.yaml conda
    wrappers/mosdepth/environment.yaml conda
    wrappers/multiqc/environment.yaml conda
    wrappers/picard/addorreplacereadgroups/environment.yaml conda
    wrappers/picard/collectalignmentsummarymetrics/environment.yaml conda
    wrappers/picard/collecthsmetrics/environment.yaml conda
    wrappers/picard/collectinsertsizemetrics/environment.yaml conda
    wrappers/picard/collecttargetedpcrmetrics/environment.yaml conda
    wrappers/picard/createsequencedictionary/environment.yaml conda
    wrappers/picard/gathervcfs/environment.yaml conda
    wrappers/picard/markduplicates/environment.yaml conda
    wrappers/picard/mergesamfiles/environment.yaml conda
    wrappers/picard/mergevcfs/environment.yaml conda
    wrappers/picard/revertsam/environment.yaml conda
    wrappers/picard/samtofastq/environment.yaml conda
    wrappers/picard/sortsam/environment.yaml conda
    wrappers/platypus/environment.yaml conda
    wrappers/reference/ensembl-annotation/environment.yaml conda
    wrappers/reference/ensembl-sequence/environment.yaml conda
    wrappers/reference/ensembl-variation/environment.yaml conda
    wrappers/rtg-tools/vcfeval/environment.yaml conda
    wrappers/samblaster/environment.yaml conda
    wrappers/samtools/bam2fq/interleaved/environment.yaml conda
    wrappers/samtools/bam2fq/separate/environment.yaml conda
    wrappers/samtools/depth/environment.yaml conda
    wrappers/samtools/faidx/environment.yaml conda
    wrappers/samtools/fastq/environment.yaml conda
    wrappers/samtools/fixmate/environment.yaml conda
    wrappers/samtools/flagstat/environment.yaml conda
    wrappers/samtools/idxstats/environment.yaml conda
    wrappers/samtools/index/environment.yaml conda
    wrappers/samtools/merge/environment.yaml conda
    wrappers/samtools/mpileup/environment.yaml conda
    wrappers/samtools/sort/environment.yaml conda
    wrappers/samtools/stats/environment.yaml conda
    wrappers/samtools/view/environment.yaml conda
    wrappers/smoove/environment.yaml conda
    wrappers/snpeff/environment.yaml conda
    wrappers/tabix/environment.yaml conda
    wrappers/vcf2db/environment.yaml conda
    wrappers/vcfanno/environment.yaml conda
    wrappers/vcflib/environment.yaml conda
    wrappers/vcftools/filter/environment.yaml conda
    wrappers/vep/environment.yaml conda
    wrappers/verifybamid2/environment.yaml conda
    wrappers/vt/environment.yaml conda
    • vt 2015.11.10
    wrappers/wham/environment.yaml conda
    • wham 1.8.0.1.2017.05.03
    wrappers/gatk/filtermutectcalls/environment.yaml conda
    wrappers/mity/call/environment.yaml conda
    wrappers/mity/normalise/environment.yaml conda
    wrappers/mity/report/environment.yaml conda
    wrappers/peddy/environment.yaml conda
    wrappers/report_upload/PT_identifier/environment.yaml conda
    wrappers/report_upload/post_report/environment.yaml conda
    wrappers/rtg-tools/vcfsubset/environment.yaml conda
    wrappers/samtools/markdup/environment.yaml conda