males_variant calling

Males variant calling (N = 479)

Folder: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lycaeides_dubois/Variants

lycaeidesMalesBam.txt = id list for males

males_variantsLycaeides.bcf/vcf = variant files for males

#get number of variants called:

grep '^Sc' males_variantsLycaeides.vcf | wc -l #860229

OR

bcftools stats males_variantsLycaeides.vcf > maleslycaeides.stats

#filter variants 1

perl vcfFilter_af.pl males_variantsLycaeides.vcf4

Number of variants retained after this round of filtering = 82845

##filter variants 2

grep ^Sc males_filtered2x_variantsLycaeides.vcf | cut -f 8 | cut -d ';' -f 1| grep -o '[0-9]*' > depth_filtered2X_males.txt

grep ^Sc males_filtered2x_variantsLycaeides.vcf | cut -f 1 | cut -d '_' -f 2 | cut -d ';' -f 1 > scaffold_males.txt

grep ^Sc males_filtered2x_variantsLycaeides.vcf | cut -f 2 > positions_males.txt

paste scaffold_males.txt positions_males.txt > snpsMales.txt

#max coverage = 9710.95

perl ../filterSomeMore.pl #52950