{"repo":"nf-core/rnavar","free":true,"listed":false,"github":"https://github.com/nf-core/rnavar","clone":"git clone https://github.com/nf-core/rnavar.git","description":"gatk4 RNA variant calling pipeline","language":"Nextflow","stars":61,"topics":["gatk4","variant-calling","rnaseq","rna","worflow","pipeline","nextflow","nf-core","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/rnavar is a bioinformatics pipeline for RNA variant calling analysis following GATK4 best practices. Pipeline summary 1. Merge re-sequenced FastQ files ( cat ) 2. Read QC ( FastQC ) 3. (Optionally) Extract UMIs from FASTQ reads ( UMI-tools ) 4. (Optionally) HLATyping from FASTQ reads ( Seq2HLA ) 5. Align reads to reference genome ( STAR ) 6. Sort and index alignments ( SAMtools ) 7. Duplicate read marking ( Picard MarkDuplicates ) 8. Scatter one interval-list into many interval-files ( GATK4 IntervalListTools ) 9. Splits reads that contain Ns in their cigar string ( GATK4 SplitNCigarReads ) 10. Estimate and correct systematic bias using base quality score recalibration ( GATK4 BaseRecalibrator , GATK4 ApplyBQSR ) 11. Convert a BED file to a Picard Interval List ( GATK4 BedToIntervalList ) 12. Call SNPs and indels ( GATK4 HaplotypeCaller ) 13. Merge multiple VCF files into one VCF ( GATK4 MergeVCFs ) 14. Index the VCF ( Tabix ) 15. Filter variant calls based on certain criteria ( GATK4 VariantFiltration ) 16. Annotate variants ( BCFtools Annotate , snpEff , Ensembl VEP) 17. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ( MultiQC , R ) Summary of tools and version used in the pipeline Tool Version ---------- ------- BCFTools 1.22 BEDTools 2.31.1 cat 9.5 EnsemblVEP 115.2 FastQC 0.12.1 GATK 4.6.2.0 GffRead 0.12.7 HTSlib 1.21 Mosdepth 0.3.10 MultiQC 1.33 Picard 3.4.0 SAMtools 1.22.1 Seq2HLA 2.3 SnpEff 5.3.0a","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/rnavar/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}