I got a sorted BAM file from an alignment of an NGS output with a human reference genome from NCBI. I need to figure out what is the sex of the person from which the sample was extracted. I found that it's done with Samtools coverage command. If it's a male, the X chromosome's coverage is expected to be roughly half of the coverage of an autosomal chromosomes. I run this command but the output was not as I expected. The output has 639 rows. From what I saw online the number of rows needs to be the same as the chromosomes number, and it's an NGS output for a human.
Here's an excerpt from the output:
With the help of WouterDeCoster I found that rows 63 and 64 in the image are of chromosomes X and Y, respectively. Yet I'm not sure if it's a male or a female. According to [this website][2], in males the coverage in the X and Y chromosomes should be roughly half the coverage in autosomal chromosomes, since males have only one copy of X and one of Y, unlike autosomal chromosomes copies, of which they have two. In females the coverage on Y should be zero and on X it should be roughly the same as in autosomal. In my data, none of these two options qualify. If I had to guess I would say it's a woman since the X coverage is almost the same as in other chromosomes, but the Y coverage is definitely not zero.
Any opinions will be welcomed. Thanks!
The first column are chromosomes, but are using a less commonly used identifier system (accession ids). You can find that here:
https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39 (scroll down a bit until you see the table titled "Assembly Unit: Primary Assembly (GCF_000001305.15)").
Thanks. That's where I got the reference genome. I hope I'll find answers there.
The answer is there, too.
The answer comes from the fact that a Y chromosome couldn't be found (unlocalized)?