.DS_Store
annotation/**/*.vcf.{gz,gz.tbi}
csv/*.csv
multiqc/multiqc_data/multiqc.parquet
multiqc/multiqc_data/bcftools*.txt
multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt
multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt
multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt
multiqc/multiqc_data/gatk_base_recalibrator.txt
multiqc/multiqc_data/llms-full.txt
multiqc/multiqc_data/mosdepth_cov_dist.txt
multiqc/multiqc_data/mosdepth_cumcov_dist.txt
multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc_bcftools_stats.txt
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_general_stats.txt
multiqc/multiqc_data/multiqc_picard_dups.txt
multiqc/multiqc_data/multiqc_samtools_stats.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/picard_deduplication.txt
multiqc/multiqc_data/vcftools*.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
no_intervals.{bed,bed.gz,bed.gz.tbi}
pipeline_info/*.{html,json,txt,yml}
preprocessing/**/*.{bam,bam.bai,cram,cram.crai,table}
reference/dragmap/hash_table.{cfg,cfg.bin}
reference/dragmap/hash_table_stats.txt
reports/**/*.cram.metrics{,.multiqc.tsv}
reports/EnsemblVEP/*/*.ann.summary.html
reports/fastp/**/*.fastp.{log,html}
reports/fastqc/**/*_fastqc.{html,zip}
reports/ngscheckmate/ngscheckmate.pdf
reports/ngscheckmate/vcfs/*.ngscheckmate.vcf.gz
reports/samtools/**/**.cram.stats
reports/snpeff/*/*_snpEff.csv
reports/snpeff/*/snpEff_summary.html
reports/vcftools/**/*.TsTv.qual
variant_calling/**/*.{bcf,vcf,vcf.gz,vcf.gz.tbi}
variant_calling/ascat/*/*.metrics.txt
variant_calling/**/*.{pdf,png}
variant_calling/controlfreec/*/config.txt
variant_calling/msisensor2/*/*_somatic
variant_calling/muse/*/*.MuSE.txt
variant_calling/mutect2/*/*.mutect2.artifactprior.tar.gz
variant_calling/tiddit/*/*.tiddit.ploidies.tab
variant_calling/varlociraptor/*/*.alignment-properties.json
