How to analyze NGS data in Nexus

This post deals with loading NGS data into Nexus for copy number variation and structural variants.

BAM files produced from NGS have to be processed before loading into Nexus. Variant calls in VCF format can be loaded into the next version of Nexus to be released shortly. VCF files can be created from BAM files with tools like GATK Or VarScan Or samtools mpileup option.

For Exome data, where matching sample and reference BAM files are present, Dr Sean Davis’ Python script ngCGH can be used to create a text file (with log2ratio of read-depth counts) and loaded into Nexus with NGS custom data type for copy number. More details can be seen in this webinar.

Details on running the Python script are available at:

http://github.com/seandavi/ngs
https://github.com/seandavi/ngs/blob/master/scripts/ngCGH.py

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