aneuploidy detection in DNA sequencing

Question

[joerodger2017]

I am planning to perform DNA seq for detection of aneluploidy condition in circulatory DNA. Is there a set rule how much sequencing depth should be used. Secondly I read few papers but could not find a set software to detect aneluploidy from DNA sequencing. Is there a set software or tool that can be useful. Any suggestion will be helpful. I am working with human genome and using Illumina nex seq platform for whole genome DNA seq.

Thanks

[WouterDeCoster]

Please add information with regard to the organism you are working on and the sequencing technology you are planning to use.

[joerodger2017]

My Bad. I have edited information in original post.

Answer 1

[willgilks]

Hi joerodger2017

I'm not sure what the minimum depth you use is. Maybe you could sequence the same individual at different depths as a pilot study.

To count the number of reads mapping to each chromosome, you can use the command: samtools idxstats alignments.bam (http://samtools.sourceforge.net/). Divide this number by the length of each chromosome to get a reads-per-base for each chromosome. This value is the same across all autosomes of an individual (low variance) ... unless there is a gain or loss of material. Sex chromosome dosage could be incorporated.

To detect sub-chromosomal structural variation, you could use the CNV-detection program, Genomestrip, except adjust the settings so that only really large events are screened-for, http://software.broadinstitute.org/software/genomestrip/ . I used it more generally with open-acces code, here https://f1000research.com/articles/5-2644/v3.

[WouterDeCoster]

I'm not sure what the minimum depth you use is. Maybe you could sequence the same individual at different depths as a pilot study.

Less expensive solution: sequence an individual once and use in silico downsampling to estimate required/sufficient depths.