Table of Contents : Data visualization :
Viewing BAM alignment files | Private annotations

Viewing BAM Alignments


Alamut® Visual BAM viewer main features:

In this section:


Loading BAM alignments

Two options are available to load alignment files:

Using CRAM files usually requires defining the location of reference sequences. See CRAM settings


BAM viewer components

When zooming at nucleotide level the genomic reference sequence is displayed above the targets sub-track:


Basic visualization options


General options


Viewing variants

Single nucleotide variants (SNVs) are automatically detected where non-reference bases are called at a frequency above the 'Allele frequency threshold' defined in the Preferences panel. Jump from one SNV to the other by clicking the arrow buttons on the left of the coverage sub-track:

You can also load called variants from VCF files and, now, gVCF files.

You have two possibilities to load VCF files:

This creates a sub-track above the reference sequence. Jump from one variant to the other by clicking the arrow buttons on the left.


Viewing sequencing targets

In Alamut® Visual, sequencing targets are supposed to cover current gene's exons with some exon-flanking intronic bases (20bp, by default).

You can also load targeted regions from BED files in the BAM track. You have two possibilities to load BED files:

The sub-track named "Targets" is updated with your BED defined targets.


Viewing BAM alignment statistics

Alamut® Visual computes descriptive statistics from BAM file (depth of coverage and insert size). These statistics are computed for the current displayed gene locus.

Click on the picture and, then select either "Depth of Coverage" or "Insert Size Distribution" from the menu.


CRAM settings

This section is rather technical. Help from bioinformaticians could be beneficial to define appropriate CRAM settings.

CRAM handling in Alamut is based on Samtools.

As explained here Samtools needs the reference genome sequence in order to decode a CRAM file. It uses the MD5 sum of each reference sequence as the key to link a CRAM file to the reference genome used to generate it (see also the Samtools man page).

Samtools can use either the REF_PATH or REF_CACHE environment variables to find reference sequences. Input fields for these variables are available in menu Tools > Options > Misc tab: CRAM Settings, as shown below.

You will need to provide the path to MD5 reference sequences in one of these fields (unless you use CRAM files with embedded reference sequences).

For your convenience we have prepared a package of reference MD5 files for GRCh37 and GRCh38 primary sequences. It is available here:
http://downloads.interactive-biosoftware.com/CRAM/RefCache.tgz (uncompress and untar this file)

If you use this MD5 reference directory and its path in your filesystem is /somepath/RefCache then in the 'Samtools REF_CACHE' field of the Alamut Options box enter: /somepath/RefCache/%2s/%2s/%s


© 2020 Interactive Biosoftware - Last modified: 30 May 2019