Aneuploidy analysis from WGS
1
1
Entering edit mode
8 weeks ago

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?

aneuploidy cnv wgs • 200 views
ADD COMMENT
0
Entering edit mode
8 weeks ago
mark.ziemann ★ 1.9k

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/

ADD COMMENT

Login before adding your answer.

Traffic: 2698 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6