{"title":"Release note 05.16.22","slug":"release-note-051622","body":"## Recently published apps\n\nWe have published the following apps in our Public Apps gallery:\n* **Cyrius** (v1.1.1, CWL1.2), a tool that genotypes CYP2D6 in WGS data. It takes WGS BAM or CRAM files and creates a TSV report with CYP2D6 alleles.\n* Two **PharmCAT** (v1.6.0, CWL1.2) tools:\n    * **PharmCAT VCF Preprocess** is a tool that takes a VCF file and prepares it for downstream processing with **PharmCAT**, and\n    * **PharmCAT**, a tool for interpreting guideline variants in VCF files.\n* Two **Biobambam2** (v2.0.183, CWL1.2) tools:\n    * **Biobambam2 Bamtofastq** that converts BAM/CRAM/SAM files to FASTQ format, and\n    * **Biobambam2 Bamseqchksum** - tool for calculating hashes for the contents of the provided alignments file.\n* Two **Cojac** (v0.2, CWL1.2) tools:\n    * **Cojac cooc-mutbamscan** is a tool that scans amplicons for mutation co-occurrence, and\n    * **Cojac cooc-tabmut** converts **Cojac cooc-mutbamscan** results (JSON, YAML) to a CSV file.\n* Six **iVar** (v1.3.1, CWL1.2) tools:\n    * **iVar trim** takes a sorted BAM file and trims reads based on quality and primers if provided.\n    * **iVar variants** takes an aligned BAM file and a Reference sequence and produces a TSV file with detected variants.\n    * **iVar filtervariants** filters variants across provided TSV replicate or sample variant files.\n    * **iVar consensus** takes an aligned BAM file and generates a FASTA file with consensus sequences and a TXT file with average base qualities.\n    * **iVar getmasked** takes a TSV file with variants generated by **iVar** tools, Primers BED file, and a TSV file with primer pair information and retrieves primers with mismatches to the reference sequence. Please note that this tool is only applicable to amplicon-based sequencing.\n    * **iVar removereads** takes a BAM file trimmed with **iVar trim**, a Primers BED file, and the Mismatch primer indices output by **iVar getmasked** and removes reads associated with identified mismatched primers.\n* **Pangolin** (v40.5, CWL1.2) (Phylogenetic Assignment of Named Global Outbreak LINeages), is a tool that takes a FASTA file with SARS-CoV-2 sequences and assigns each sequence to a Pango lineage using PangoLEARN.\n* **Picard RevertSam** (v2.25.7, CWL1.2), is a tool that reverts a BAM/SAM file to a previous state. It can be used to recreate an unaligned BAM file from aligned BAM/SAM files or restore original qualities to post-BQSR files (if original qualities were stored).","_id":"6282557ddbff380060db5f2e","changelog":[],"createdAt":"2022-05-16T13:45:33.463Z","user":{"name":"Marko Marinkovic","username":"","_id":"5767bc73bb15f40e00a28777"},"initVersion":{"version":"1.0","_id":"5773dcfc255e820e00e1cd50"},"project":"5773dcfc255e820e00e1cd4d","__v":0}

Release note 05.16.22


## Recently published apps We have published the following apps in our Public Apps gallery: * **Cyrius** (v1.1.1, CWL1.2), a tool that genotypes CYP2D6 in WGS data. It takes WGS BAM or CRAM files and creates a TSV report with CYP2D6 alleles. * Two **PharmCAT** (v1.6.0, CWL1.2) tools: * **PharmCAT VCF Preprocess** is a tool that takes a VCF file and prepares it for downstream processing with **PharmCAT**, and * **PharmCAT**, a tool for interpreting guideline variants in VCF files. * Two **Biobambam2** (v2.0.183, CWL1.2) tools: * **Biobambam2 Bamtofastq** that converts BAM/CRAM/SAM files to FASTQ format, and * **Biobambam2 Bamseqchksum** - tool for calculating hashes for the contents of the provided alignments file. * Two **Cojac** (v0.2, CWL1.2) tools: * **Cojac cooc-mutbamscan** is a tool that scans amplicons for mutation co-occurrence, and * **Cojac cooc-tabmut** converts **Cojac cooc-mutbamscan** results (JSON, YAML) to a CSV file. * Six **iVar** (v1.3.1, CWL1.2) tools: * **iVar trim** takes a sorted BAM file and trims reads based on quality and primers if provided. * **iVar variants** takes an aligned BAM file and a Reference sequence and produces a TSV file with detected variants. * **iVar filtervariants** filters variants across provided TSV replicate or sample variant files. * **iVar consensus** takes an aligned BAM file and generates a FASTA file with consensus sequences and a TXT file with average base qualities. * **iVar getmasked** takes a TSV file with variants generated by **iVar** tools, Primers BED file, and a TSV file with primer pair information and retrieves primers with mismatches to the reference sequence. Please note that this tool is only applicable to amplicon-based sequencing. * **iVar removereads** takes a BAM file trimmed with **iVar trim**, a Primers BED file, and the Mismatch primer indices output by **iVar getmasked** and removes reads associated with identified mismatched primers. * **Pangolin** (v40.5, CWL1.2) (Phylogenetic Assignment of Named Global Outbreak LINeages), is a tool that takes a FASTA file with SARS-CoV-2 sequences and assigns each sequence to a Pango lineage using PangoLEARN. * **Picard RevertSam** (v2.25.7, CWL1.2), is a tool that reverts a BAM/SAM file to a previous state. It can be used to recreate an unaligned BAM file from aligned BAM/SAM files or restore original qualities to post-BQSR files (if original qualities were stored).