Detecting Klinefelter from genomic files

Question

[paulcaiella]

Hello everyone,

I have a question: I have a set of genomic file (vcf, bam, fastq), is there a way to check if the subject has Klinefelter syndrome? I apologize if this is a silly question.

Thanks for the attention

[Bastien Hervé]

Is that the XXY disease ? My guess is, If you have an homogeneous depth over your no sexual chromosome and that you get twice the amount of reads on chrX the subject got the disease.

[paulcaiella]

Hi Bastien, how can I check if I have homogeneous coverage? I am sorry if this is a really base question, I am just approaching this field

[Bastien Hervé]

Could have be the number of mapped read per chromosome / chromosome length, or something similar. Anyway Pierre' answer is much more advance, mine is just theorical !

[paulcaiella]

Thanks for the suggestion Pierre! :-D

Answer 1

[Pierre Lindenbaum]

Klinefelter syndrome (KS) also known as 47,XXY or XXY, is the set of symptoms that result from two or more X chromosomes in males

A first idea would be to use the BAI files of your several bams (affected/non-affected) and use indexcov to quickly get a chart for the sexual chromosomes:

[paulcaiella]

Thanks for the suggestion Pierre, however I only have a single set of genomic files, regarding a single individual. Do you have any other suggestions?

[Pierre Lindenbaum]

use some BAM files from 1000 genomes as positive controls. You need the BAIs but you don't need the whole BAMs, just the headers.

you can just samtools view -H $bam > $small && cp $bam.bai $small.bai
and then copy $small and $small.bai and run indexcov on those. it only needs the bam to know the chroms.

— brent pedersen (@brent_p) June 15, 2018