cat NS9.vcf | awk '$6>=50.' | awk '{print $1" "$2" "$10}' > NS9_qual_short.vcf
cat NS9.vcf | awk '{print $1" "$2" "$10}' > NS9_short.vcf

grep chr1[^_,0-9] NS9_short.vcf > NS9_short1.vcf
grep chr2[^_,0-9] NS9_short.vcf > NS9_short2.vcf
grep chr3[^_,0-9] NS9_short.vcf > NS9_short3.vcf
grep chr4[^_,0-9] NS9_short.vcf > NS9_short4.vcf
grep chr5[^_,0-9] NS9_short.vcf > NS9_short5.vcf
grep chr6[^_,0-9] NS9_short.vcf > NS9_short6.vcf
grep chr7[^_,0-9] NS9_short.vcf > NS9_short7.vcf
grep chr8[^_,0-9] NS9_short.vcf > NS9_short8.vcf
grep chr9[^_,0-9] NS9_short.vcf > NS9_short9.vcf
grep chr10[^_,0-9] NS9_short.vcf > NS9_short10.vcf
grep chr11[^_,0-9] NS9_short.vcf > NS9_short11.vcf
grep chr12[^_,0-9] NS9_short.vcf > NS9_short12.vcf
grep chr13[^_,0-9] NS9_short.vcf > NS9_short13.vcf
grep chr14[^_,0-9] NS9_short.vcf > NS9_short14.vcf
grep chr15[^_,0-9] NS9_short.vcf > NS9_short15.vcf
grep chr16[^_,0-9] NS9_short.vcf > NS9_short16.vcf
grep chr17[^_,0-9] NS9_short.vcf > NS9_short17.vcf
grep chr18[^_,0-9] NS9_short.vcf > NS9_short18.vcf
grep chr19[^_,0-9] NS9_short.vcf > NS9_short19.vcf
grep chr20[^_,0-9] NS9_short.vcf > NS9_short20.vcf
grep chr21[^_,0-9] NS9_short.vcf > NS9_short21.vcf
grep chr22[^_,0-9] NS9_short.vcf > NS9_short22.vcf

filtshortvcf2 < NS9_short1.vcf > NS9_1.geno
filtshortvcf2 < NS9_short2.vcf > NS9_2.geno
filtshortvcf2 < NS9_short3.vcf > NS9_3.geno
filtshortvcf2 < NS9_short4.vcf > NS9_4.geno
filtshortvcf2 < NS9_short5.vcf > NS9_5.geno
filtshortvcf2 < NS9_short6.vcf > NS9_6.geno
filtshortvcf2 < NS9_short7.vcf > NS9_7.geno
filtshortvcf2 < NS9_short8.vcf > NS9_8.geno
filtshortvcf2 < NS9_short9.vcf > NS9_9.geno
filtshortvcf2 < NS9_short10.vcf > NS9_10.geno
filtshortvcf2 < NS9_short11.vcf > NS9_11.geno
filtshortvcf2 < NS9_short12.vcf > NS9_12.geno
filtshortvcf2 < NS9_short13.vcf > NS9_13.geno
filtshortvcf2 < NS9_short14.vcf > NS9_14.geno
filtshortvcf2 < NS9_short15.vcf > NS9_15.geno
filtshortvcf2 < NS9_short16.vcf > NS9_16.geno
filtshortvcf2 < NS9_short17.vcf > NS9_17.geno
filtshortvcf2 < NS9_short18.vcf > NS9_18.geno
filtshortvcf2 < NS9_short19.vcf > NS9_19.geno
filtshortvcf2 < NS9_short20.vcf > NS9_20.geno
filtshortvcf2 < NS9_short21.vcf > NS9_21.geno
filtshortvcf2 < NS9_short22.vcf > NS9_22.geno
