I'm Lynn. I have a question. Currently, we are doing the annotation and alignment for whole human genome using GATK tools. But we noticed that the chrY is still appeared even the sample is female. When we do the downstream analysis, (eg.:snpeff) the output still shows the chrY in the female subject.
We wonder how can we exclude the chrY and only get the chrX for female samples. Is there any specific command that we need to put in the command line?
I am really new to the field of genome analysis (I've got a computer science background). At the moment I am dealing with the topic of variant calling and decided to use / understand the HaplotypeCaller. So please apologize my stupid question.. I do not understand why the HaplotypeCaller does the whole alignment step again (or did I understand that wrong?). What is the purpose to use the BAM file and re-align it?
Best regards, Kristina