cat NS12.vcf | awk '$6>=50.' | awk '{print $1" "$2" "$10}' > NS12_qual_short.vcf
cat NS12.vcf | awk '{print $1" "$2" "$10}' > NS12_short.vcf

grep chr1[^_,0-9] NS12_short.vcf > NS12_short1.vcf
grep chr2[^_,0-9] NS12_short.vcf > NS12_short2.vcf
grep chr3[^_,0-9] NS12_short.vcf > NS12_short3.vcf
grep chr4[^_,0-9] NS12_short.vcf > NS12_short4.vcf
grep chr5[^_,0-9] NS12_short.vcf > NS12_short5.vcf
grep chr6[^_,0-9] NS12_short.vcf > NS12_short6.vcf
grep chr7[^_,0-9] NS12_short.vcf > NS12_short7.vcf
grep chr8[^_,0-9] NS12_short.vcf > NS12_short8.vcf
grep chr9[^_,0-9] NS12_short.vcf > NS12_short9.vcf
grep chr10[^_,0-9] NS12_short.vcf > NS12_short10.vcf
grep chr11[^_,0-9] NS12_short.vcf > NS12_short11.vcf
grep chr12[^_,0-9] NS12_short.vcf > NS12_short12.vcf
grep chr13[^_,0-9] NS12_short.vcf > NS12_short13.vcf
grep chr14[^_,0-9] NS12_short.vcf > NS12_short14.vcf
grep chr15[^_,0-9] NS12_short.vcf > NS12_short15.vcf
grep chr16[^_,0-9] NS12_short.vcf > NS12_short16.vcf
grep chr17[^_,0-9] NS12_short.vcf > NS12_short17.vcf
grep chr18[^_,0-9] NS12_short.vcf > NS12_short18.vcf
grep chr19[^_,0-9] NS12_short.vcf > NS12_short19.vcf
grep chr20[^_,0-9] NS12_short.vcf > NS12_short20.vcf
grep chr21[^_,0-9] NS12_short.vcf > NS12_short21.vcf
grep chr22[^_,0-9] NS12_short.vcf > NS12_short22.vcf

filtshortvcf2 < NS12_short1.vcf > NS12_1.geno
filtshortvcf2 < NS12_short2.vcf > NS12_2.geno
filtshortvcf2 < NS12_short3.vcf > NS12_3.geno
filtshortvcf2 < NS12_short4.vcf > NS12_4.geno
filtshortvcf2 < NS12_short5.vcf > NS12_5.geno
filtshortvcf2 < NS12_short6.vcf > NS12_6.geno
filtshortvcf2 < NS12_short7.vcf > NS12_7.geno
filtshortvcf2 < NS12_short8.vcf > NS12_8.geno
filtshortvcf2 < NS12_short9.vcf > NS12_9.geno
filtshortvcf2 < NS12_short10.vcf > NS12_10.geno
filtshortvcf2 < NS12_short11.vcf > NS12_11.geno
filtshortvcf2 < NS12_short12.vcf > NS12_12.geno
filtshortvcf2 < NS12_short13.vcf > NS12_13.geno
filtshortvcf2 < NS12_short14.vcf > NS12_14.geno
filtshortvcf2 < NS12_short15.vcf > NS12_15.geno
filtshortvcf2 < NS12_short16.vcf > NS12_16.geno
filtshortvcf2 < NS12_short17.vcf > NS12_17.geno
filtshortvcf2 < NS12_short18.vcf > NS12_18.geno
filtshortvcf2 < NS12_short19.vcf > NS12_19.geno
filtshortvcf2 < NS12_short20.vcf > NS12_20.geno
filtshortvcf2 < NS12_short21.vcf > NS12_21.geno
filtshortvcf2 < NS12_short22.vcf > NS12_22.geno
