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executable file 17 lines (12 sloc) 0.322 kb
#!/bin/bash
### Script to parse vcf file and not allow for missing data.
INFILE=$1
OUTFILE=$2
grep -v -m 1 '##' $INFILE >> $OUTFILE
while read line
do
if [[ "$line" == *"PASS"* ]] && [[ "$line" == *"FS=0.000"* ]] && [[ "$line" != *"./."* ]]
then
printf "%s\n" "$line" >> $OUTFILE
fi
done < $INFILE
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