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quartet_dna_quality_control_wes_big_pipeline
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quartet_dna_quality_control.../codescripts/linux_command.sh

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  1. cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"$7"\t.\t.\t.\tGT\t"$6}' | grep -v '2_y' > LCL5.body

  2. cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"$15"\t.\t.\t.\tGT\t"$14}' | grep -v '2_y' > LCL6.body

  3. cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"$23"\t.\t.\t.\tGT\t"$22}' | grep -v '2_y' > LCL7.body

  4. cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"$31"\t.\t.\t.\tGT\t"$30}' | grep -v '2_y' > LCL8.body

  5. 

  6. for i in *txt; do cat $i | awk '{ if ((length($3) == 1) && (length($4) == 1)) { print } }' | grep -v '#' | cut -f3,4 | sort |uniq -c | sed 's/\s\+/\t/g' | cut -f2 > $i.mut; done