Craete GATK compatible dbSNP file

$ lftp ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz

$ gunzip 00-All.vcf.gz

$ grep -c '#' 00-All.vcf

57

$ tail -n+58 00-All.vcf | awk '$0 !~ "_random" {print}' | awk '$0 !~ "_hap" {print}'| awk '$0 !~ "PAR" {print}' | awk '{sub(/MT/, "M", $0); print}' | awk '{print "chr" $0}'> dbsnp132.human.body.vcf

$ awk '{print $1}' dbsnp132.human.body.vcf | sort -u

chr1

chr10

chr11

chr12

chr13

chr14

chr15

chr16

chr17

chr18

chr19

chr2

chr20

chr21

chr22

chr3

chr4

chr5

chr6

chr7

chr8

chr9

chrM

chrX

chrY

$ head -n 57 00-All.vcf > dbsnp132.human.head.vcf

$ cat dbsnp132.human.head.vcf dbsnp132.human.body.vcf > dbsnp132.human.vcf

$ rm dbsnp132.human.body.vcf dbsnp132.human.head.vcf