Computational biology and genomics
I was updating my BAM to CRAM post spurred on by a recent comment and then I wondered whether I could store my FASTQ files as unaligned CRAM files to save space. I thought it wouldn’t be possible because the reads are unaligned and therefore we can’t make use of a reference to save space…
The SAMtools mpileup utility provides a summary of the coverage of mapped reads on a reference sequence at a single base pair resolution. In addition, the output from mpileup can be piped to BCFtools to call genomic variants. I’m currently working with some Sanger sequenced PCR products, which I would like to call variants on….
I’ve tried to explain the BAM flags to my colleagues and I think each time I have left them more confused. So perhaps I can do a better job of explaining BAM flags in writing. For this post, I will use this BAM file from the 1000 Genomes Project: NA18553.chrom11.ILLUMINA.bwa.CHB.low_coverage.20120522.bam.