Workflow Wednesdays – Coverage analysis 1.

25/09/2013

Nowadays, when whole exome and whole genome alignments are becoming fairly routine and even gene panels often target hundreds of genes, it’s no longer a valid option for researchers to visually check the quality of alignments. Generating coverage measures and statistics is a good tool for identifying sequencing or...

Workflow Wednesdays – Extracting reads from an alignment file

18/09/2013

If you work with sam/bam files regularly, sooner or later you’ll end up trying to get a subset of an alignment. There can be several reasons for doing this: you might want to remove off-target reads, investigate alignment problems or just get rid off parts that you’re not interested...

Workflow Wednesdays – Sorting alignments

11/09/2013

Most variant calling softwares require sorted alignments as an input. There are two main ways to sort a SAM or BAM file: you can sort the lines by read names or you can sort the aligned reads by leftmost coordinates.

Workflow Wednesdays – Alignments – Format conversion

04/09/2013

I could go on forever and ever about different short read aligners, but I think you get the gist of it. So let’s talk about alignment files! Most modern reference based aligners produce their output in sam format. If you’re not familiar with this file format, check out my...

Bioinformatics for Beginners – File Formats Part 3. – Alignments

08/07/2013

The generally used file formats for sequence based alignments are the SAM and BAM formats. These files can contain information about mapped and unmapped reads, the contigs of the reference sequence that was used and many more things. SAM You can find the SAM format specification here and the...