basic stats that can be gleaned from VCF file output from GATK

runVCFstats.sh

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+#!/bin/bash
+
+module use /shared/software/GIF/modules/
+module use  /shared/modulefiles
+module load vcftools
+module load compilers/gcc-4.8.2 
+
+out=`basename $1`
+#filter out undesirable lines create new vcf file
+#vcftools --vcf $1 --remove-indv 6497 --remove-indv 7074 --non-ref-ac-any 1 --recode
+
+
+#snp count
+grep -v "#" $1 | wc -l > ${out}.snpcount
+
+#determine the depth of coverage by individual
+vcftools --vcf $1  --depth --out ${out}
+
+#determine Transitions and transversion ratio Ts/Tv
+vcftools --temp ./temp  --vcf $1  --TsTv 1000
+#explore potential bins of interest
+#awk '$NF<1 && $NF>0' out.TsTv | awk '{print $1,$2}' | intervalBins.awk 10000 | awk '$3>3'
+#awk '$NF>4' out.TsTv | awk '{print $1,$2}' | intervalBins.awk 10000 | awk '$3>2'
+
+#determine windowed pi values
+vcftools --temp ./temp  --vcf $1  --window-pi 1000 --window-pi-step 1000 --out ${out}_1000
+vcftools --temp ./temp  --vcf $1  --window-pi 10000 --window-pi-step 1000 --out ${out}_10000
+
+#singleton enrichment in bins could indicate regions of interest.
+vcftools --temp ./temp  --vcf $1  --singletons --out ${out}
+
+#look at relatedness
+vcftools --vcf $1  --relatedness --out ${out}
+
+#missing site frequency for potential filtering purposes on a per site and overall individual basis
+vcftools --vcf $1   --missing-site --out ${out}
+vcftools --vcf $1  --missing-indv --out ${out}
+
+#SNP density
+vcftools --vcf $1  --SNPdensity 1000 --out ${out}_1000
+vcftools --vcf $1  --SNPdensity 10000 --out ${out}_10000
+
+#Tajima's D 
+vcftools --vcf $1  --TajimaD 1000 --out ${out}_1000
+vcftools --vcf $1  --TajimaD 10000 --out ${out}_10000
+
+#inbreeding coefficient
+vcftools --vcf $1  --het --out ${out}
+