Vcf2maf.md

awk '!/^#/ {gsub(/^chr/, "", $1)} 1' /home/benson/project/WGS-report/WGS_data/test/NGS2401027.vcf \

/home/benson/project/WGS-report/WGS_data/test/NGS2401027.nochr.vcf

zcat /home/benson/project/WGS-report/WGS_data/test/NGS2401027.hard-filtered.vcf.gz | awk '!/^#/ {gsub(/^chr/, "", $1)} 1' \

/home/benson/project/WGS-report/WGS_data/test/NGS2401027.nochr.vcf

取出 header

grep "^#" /home/benson/project/WGS-report/WGS_data/test/NGS2401027.nochr.vcf > header.vcf

取出前 5000 筆非註解（變異）行

grep -v "^#" /home/benson/project/WGS-report/WGS_data/test/NGS2401027.nochr.vcf | head -n 5000 > body.vcf

合併為測試用 VCF

cat header.vcf body.vcf > /home/benson/project/WGS-report/WGS_data/test/NGS2401027.head5000.vcf

awk 'BEGIN{FS=OFS="\t"} /^#/ || $1 ~ /^(MT|[1-9]|1[0-9]|2[0-2]|X|Y)$/ {print}' /home/benson/project/WGS-report/WGS_data/test/NGS2401027.head5000.vcf \

/home/benson/project/WGS-report/WGS_data/test/NGS2401027.head5000.primary.vcf