Determine the sex of a sample from a .vcf

Question

[Gl_14]

Hi everyone, I am doing my thesis internship and I need some help: I have the .vcf of 110 patients and I would like to determine their sex. I read it could be done taking into account the depth of coverage of the sexual chromosomes, but I have no idea on how to do it; could someone tell me if there's a software that allows me to do this, using the vcf files as input? thank you

Answer 1

[4galaxy77]

plink --check-sex should be what you need, assuming you have data on the x-chromosome. I always prefer to recode the vcf to plink format first and then run the sex check.

https://www.cog-genomics.org/plink/1.9/basic_stats#check_sex

Id try something like this

plink --vcf data.vcf --make-bed --out data
plink --bfile data --check-sex --out data.sex_check

[Gl_14]

thank you very much! I am not familiar with plink, but I'll try to use it!

[Gl_14]

sorry for bothering you again, but I downloaded plink 1.90 beta (build: Stable (beta 6.21, 19 Oct)) and there's no "--vcf" neither "--make-bed" option in it, how can I add them? I do not find them in the "manual" page (typing "man plink"). Thanks

[4galaxy77]

What happens when you type plink --vcf

[Gl_14]

"plink: unknown option "--vcf" "

[chrchang523]

That means you aren't running plink 1.9 (you can also run "plink --version" to check). Check your system PATH against where you placed the downloaded program, and where any other programs named "plink" may be.

Answer 2

[prasundutta87]

You would need the SAM/BAM/CRAM files of the patients. Just check the total number of reads aligned to the X-chromosome. Since females have two X-chromosomes and males have one, the number of reads aligned to the X-chromosome of the female samples will be roughly double to the number of reads aligned to the X-chromosome of the male samples.

Run Samtools idxstats (http://www.htslib.org/doc/samtools-idxstats.html) on your BAM/SAM/CRAM file. The output is TAB-delimited with each line consisting of reference sequence name, sequence length, # mapped read-segments and # unmapped read-segments. You need the mapped read-segments information of the X-chromosome of all the samples to perform the above described procedure.

Of course, this is just one of the many ways you can approach this problem.

[Gl_14]

Unfortunately, I can only have access to the .vcf for each sample, not to the BAM files; however, if I cannot find a way to use them, I'll try to ask for BAM files access. Thank you a lot!

[prasundutta87]

Dealing with VCFs to get depth of coverage information on sex chromosomes can be a little tricky due to the presence of pseudoautosomal regions (PAR). You can get into that if getting access to alignment files becomes difficult.

This post may be helpful as well: Determine sex from vcf file (or sequencing data)

[Gl_14]

Thanks a lot again!