SAMtools

[…] PRINSEQ-lite (version 0.20.4). Resulting high-quality reads were simultaneously mapped against the Mus musculus (GRCm38) and Drosophila melanogaster (dm6) reference genomes via BWA (version 0.7.15). SAMtools (version 1.4) was used to split the alignments into mouse and Drosophila reads. Read normalization via the Drosophila melanogaster spike-in material was carried out with Deeptools (version 2. […]

[…] of the chromosome was derived from both S799 and YPH499, the mutation was annotated as a BIR, and rearranged positions were further searched from the chimera sequences around the events using BLAST, samtools (http://samtools.sourceforge.net/), and perl/shell scripts. Partial chimeric sequences from the pair within a chromosome were annotated as SGCs. Because homologous TLs, BIRs, and SGCs represe […]

[…] Sequence reads were mapped to the human genome (hg19) using Burrows-Wheeler Alignment tool. Duplicate read removal was performed using Picard and Samtools, and local alignment was optimized by The Genome Analysis Toolkit. Variant calling was only performed in targeted regions of CancerSCAN. Somatic variant calling of each tumor was based on the […]

[…] using the accession numbers in Supplementary Fig.  and B, aligned to the reference genome hg19 for HCT116 cells and mm8 for mouse liver using Bowtie2, and filtered according to alignment scores using SAMtools. SRA files were converted to FASTQ format using the command fastq-dump in the SRA Toolkit (https://github.com/ncbi/sra-tools) before the alignment. Peaks were called using MACS2 without the – […]

[…] uality trimmed using FastQC (v0.11.5) and mapped to the mouse genome (mm9) using Bismark (v0.16.3) using the following options: “–bam –chunkmbs 1024 –multicore 8”. Mapped BAM files were sorted with SAMtools (v0.1.19-96b5f2294a) and methylation calls were extracted using the “Rsamtools” (v.1.22.0) and “data.table” (v.1.9.6) packages, as well as custom R scripts as previously described. Coverage w […]

[…] and InDels was done using GATK Unified Genotyper, which uses a Bayesian genotype likelihood model to report alleles and Phred-scaled confidence values []. Variants (SNVs and indels) were called with SAMTools, with reference to public databases including dbSNP and 1000Genomes and gnomAD []. Analysis was performed with preference to variants located in genes implicated in atypical non-autoimmune fo […]