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Making the Call

MassGenomic's Dan Koboldt discusses his latest Bioinformatics paper. In it, he presents VarScan, which is a program he developed to call SNPs and indels from next-gen sequencing data. The two main challenges to making accurate calls are telling the difference between real variants and false positives in short reads and holding the volume of data. "VarScan detects sequence variants, combines them by position and type, and then computes the read counts, average base quality, and number of strands supporting each allele," Kolbodt says. He later adds that most SNPs called by VarScan were in dbSNP, supported by Illumina/Solexa calls, or both.

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

US to Make More Vaccines for Monkeypox Available

The US is to make nearly 300,000 vaccine doses available in the coming weeks to stem the spread of human monkeypox virus, according to NPR.

Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.