<big>Advanced variant caller for exome and whole genome sequencing data including next-generation sequencing (NGS).</big>This app combines powerful cloud computing with SamTools for variant calling. It analyzes a BAM file and generates a VCF file that contains a list of identified variants including genotype calls and likelihoods. <h3>Use this app to detect the following types of variants in BAM files from whole genome sequencing (WGS) and exome sequencing: </h3><ul><li>SNPs</li><li>multinucleotide variants (also known as MNPs)</li><li>deletions and insertions (DIPs) that are less than one read length</li>
</ul> <h3>Compatibility Information</h3>This app is only compatible with BAM files obtained from genome sequencing. When this app is started, only BAM files (filenames that end with .bam) will be able to be selected.

<ol style="margin-left:40px"><li>Start the app</li><li>Select a BAM file <ul><li>You can select any BAM file in your account. This includes files you've uploaded, files generated by one or your apps and files that have been shared with you by others.</li></ul></li><li>Select the BAM file's reference genome. <ul><li>Alternatively, you can choose 'Auto-detect' and your file's reference genome will be automatically determined.</li></ul></li><li>Click submit</li>
</ol>You'll receive an email notification with a link to the app results, which will be a downloadable VCF file. The VCF file will be stored in your account and you can also use it with other apps.

Li H, et al and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics (25), 2078-9. [<a href="https://www.ncbi.nlm.nih.gov/pubmed/19505943" >19505943</a>]Li H, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics (2011) 27(21) 2987-93. [<a href="https://www.ncbi.nlm.nih.gov/pubmed/21903627" >21903627</a>]Li H, Mathematical Notes on SAMtools Algorithms (2010) [<a href="https://www.broadinstitute.org/gatk/media/docs/Samtools.pdf" >link</a>]Danecek P, et al. Multiallelic calling model in bcftools (-m) (2014) [<a href="https://samtools.github.io/bcftools/call-m.pdf" >link</a>]Narasimhan V, et al. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data, Bioinformatics (2016) 32(11) 1749-51 [<a href="https://www.ncbi.nlm.nih.gov/pubmed/26826718" >26826718</a>]Danecek P, et al. A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data, PLoS One (2016) 11(5) e0155014 [<a href="https://www.ncbi.nlm.nih.gov/pubmed/27176002" >27176002</a>]Danecek P, et al. BCFtools/csq: Haplotype-aware variant consequences, Bioinformatics (2017) 33(13) 2037-39 [<a href="https://www.ncbi.nlm.nih.gov/pubmed/28205675" >28205675</a>]

Variant Discovery

Advanced variant caller for exome and whole genome sequencing data including next-generation sequencing (NGS).