BAMSurgeon

[…] riants or CNAs only. Moreover, in all these methods, simulated variants are based on the addition of synthetic elements that do not mimic the sequencing technologies biases. Finally, only tHAPMix and BAMSurgeon are able to produce results in.bam format, while the other tools output reads in fasta/fastQ formats that need to be aligned against a reference genome. […]

[…] tes, strand bias and GC content[]; factors that can be more variable for exome and targeted sequencing data particularly when derived from clinical specimens. Recently, Ewing et al. developed a tool, BAMSurgeon, to introduce synthetic mutations into existing reads in a Binary alignment Mapping (BAM) file[]. BAMSurgeon provides support for adjusting variant allele fractions (VAF) of engineered muta […]

[…] simulators with built-in or user-supplied error models such as ART  and SeqMaker . Alternatively, hybrid datasets featuring real reads and simulated variants at arbitrary VAFs can be generated using BAMSurgeon . Synthetic reads can be generated in large scale, at virtually no cost, and most importantly, contain known variants. However, synthetic data alone are generally considered inadequate beca […]

[…] tion of the synthetic tumours and their properties are fully detailed in Ewing et al. []. Briefly, high coverage binary alignment map (BAM) files were obtained from cell lines HCC1143 and HCC1954 []. BAMSurgeon [] was used to randomly ‘spike-in’ germline mutations into the BAM files. Each file was then split into two: one file representing a synthetic tumour and the other file representing the mat […]

[…] to true and the minimum percent ID set to 0.70. The ability of these programs to detect new insertions of transposons relative to the reference genome was assessed by running the programs after using BamSurgeon (github.com/adamewing/bamsurgeon) to simulate 1,000 sequences of TEs in an N2 BAM file in regions without pre-existing transposons and without excessive coverage (>1,000× coverage). BamSurg […]

[…] second technical replicate was aligned to the hybrid genome, and downsampled to 60× DoC. To generate a virtual tumor, a completely known mutation profile was then introduced by BAM replacement using BAMSurgeon and the IS3 mutation set from the ICGC-TCGA DREAM Somatic Mutation Calling Challenge at a range of variant allele frequencies []. WGSS data from the NSG mouse strain generated by the The We […]