VCF manipulation (to be edited)

#how many raw snps?

$awk '!/#/ {print $0}' 7550X1.snps.raw.vcf | wc -l

3492007

#filter dbSNP member and retain PASSed SNPs.

$awk '!/#/ {print $0}' 7550X1.snps.raw.vcf | awk '$3 !~ "rs" {print $0}' | awk '$7 ~ "PASS" {print $0}' > 7550x1.nodbsnp.pass.vcf

#how many novel SNPs?

$wc -l 7550x1.nodbsnp.pass.vcf

312776

$vcf-validator 7550x1.nodbsnp.pass.vcf

#error , no header

$head -n 22 7550X1.snps.raw.vcf > head.txt

$cat head.txt 7550x1.nodbsnp.pass.vcf > 7550x1.vcf

#have to build index!

$bgzip 7550x1.vcf

$tabix -p vcf 7550x.vcf.gz

#the commom snps between x1 and x4 (affected)

$vcf-isec -n =2 7550x1.vcf.gz 7550x4.vcf.gz > x1x4.vcf

$wc -l x1x4.vcf

130480 x1x4.vcf