Hi.

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.

The command I used:

samtools coverage -o "alignment_coverage.txt" "alignment_output.sorted.bam" 

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!