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
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:
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?
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
— brent pedersen (@brent_p) June 15, 2018
and then copy $small and $small.bai and run indexcov on those. it only needs the bam to know the chroms.
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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.
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
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 !
Thanks for the suggestion Pierre! :-D