I have a large vcf file. I need to split them by chromosome for which I have used the following command below. I was able to extract and the chromosomes chr1 to chr22, but could extract chrX,chrY and chrM. How can I get the split the file for those three chromosomes?
command I used :
bgzip -c myvcf.vcf > myvcf.vcf.gz tabix -p vcf myvcf.vcf.gz tabix myvcf.vcf.gz chr1 > chr1.vcf