Aneuploidy analysis from WGS

Question

[Thierry Waltrich]

Hello,

I am a beginner to WGS. I have sequenced my genome with Nebula Genomics. I have a CRAM file, a BAM file I generated with WGSextract and a (hard-filtered?) VCF file from Nebula. I suspect I have Kleinefelter syndrome (one extra X chromossome, 47,XXY) or Mosaic Loss of Y Chromossome. Instead of doing a karyotype I wanted to analyse this with the sequencing data. I know it should be possible by analysing CNVs, but I am completely lost trying to setup tools such as CNVpytor and Canvas, getting all kinds of errors using Linux. is there an easy way to evaluate these changes? Maybe a visual tool?

Answer 1

[mark.ziemann]

You might want to consider the applications available on Illumina Basespace which are designed for both advanced and novice analysts. For example the Dragen Joint Genotyping Pipeline is advertised as detecting SV and CNV from BAM files, while the DRAGEN Germline - All Callers will search for SNV, SV, CNV, CYP2D6, HLA, SMA and Repeat Expansions. https://basespace.illumina.com/apps/