I am trying to extract a single chromosome from my dataset so that I can run analyses using only this sex chromosome and compare to results of similar analyses on the entire genome. However, all of my chromosomes are labeled as "Pseudochromosomes", i.e., the chromosome I want to extract and make it's own vcf file is "Pseudochromosome_Z". I read that the following command should do the trick for regularly named chromosomes:
grep -w '^#\|^#CHROM\|^chr[Z]' selas.dp1maxmiss50maf05f_subset_.012.vcf > Z.vcf
However, how do I do this for pseudochromosomes? Thanks for bearing with my ignorance.