# run bcftools for each chrom in the vcf
# bcftools will copy the first column and call it TGV in the VCF
# skip column 2, columns 3 and 4 have the CHROM and POS
# optional use the other columns to add other things to info for a better annotation
CHROM_NUM=10
bcftools annotate -c TGV,-,CHROM,POS,REF,ALT,-,-,-,-,-,-,-,- --annotations chr_${CHROM_NUM}_molecular_annotation.tsv.gz -h annots.hdr  ncbn.jpn.chr${CHROM_NUM}.grch38.vcf.gz 
