Call variants ============= Identify alternations of a genomic material of a sequenced individual with respect to a model, reference genome. That includes small point mutations (SNPs), small insertions and deletions. Purpose ------- * Identify genomic mutation that causes phenotypic trait of interest * Identify genomic differences between close species * Important for various genetic tests * inherited diseases * de novo mutations * oncological diseases - screening and assessing its type Required inputs --------------- * Sequenced paired-end reads from Illumina sequencer in gzipped fastq format. * each sample is represented by two gzipped fastq files * standard output files of paired-end sequencing * reference genome in fasta format :: |-- reads/original |-- _R1.fastq.gz |-- _R2.fastq.gz |-- _R1.fastq.gz |-- _R2.fastq.gz |-- reference/ |-- .fa Optional inputs --------------- * GATK ready dbSNP database in bgzipped VCF format * if the bgzipped database file has `gz` suffix it must be changed to `bgz` * required for base quality recalibration step * required for variant calling report * optional for GATK-HC variant caller * tabix index of the dbSNP database file :: |-- reference//variants |-- dbsnp.vcf.bgz |-- dbsnp.vcf.bgz.tbi Generated outputs ----------------- * List of identified variants in VCF file, filtered by user-defined criteria * Summary PDF report to assess quality of reads, mapping and variant calling Example ------- How to run example: .. code-block:: bash cd /usr/local/snakelines/example/genomic snakemake \ --snakefile ../../snakelines.snake \ --configfile config_variant_calling.yaml \ --use-conda Example configuration: .. literalinclude:: ../../example/genomic/config_variant_calling.yaml :language: yaml Planned improvements -------------------- * Call variants only in pre-defined regions (BED file) * Aggregate quality statistics of preprocess and mapping with the `MultiQC `_ * Annotation of variants * Filtering of variants based on external annotations * Interpretation of variants Included pipelines ------------------ .. toctree:: :maxdepth: 2 /pipelines/quality_report /pipelines/preprocess_paired_end /pipelines/mapping