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crazyhottommy/compare_mutect_results.sh

Created August 25, 2015 19:33
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compare mutect results overlapping
Raw
compare_mutect_results.sh
for i in {1..22} X Y
do
same=$(comm -12 <(cut -f1,2,4,5 keep_original_bam/TCGA-06-0125_$i.call.keep.txt | sort) <(cut -f1,2,4,5 keep_realigned_bam/TCGA-06-0125_$i.call.keep.txt| sort) | wc -l | tr -d " ")
original=`wc -l keep_original_bam/TCGA-06-0125_$i.call.keep.txt | awk '{print $1}'`
realigned=`wc -l keep_realigned_bam/TCGA-06-0125_$i.call.keep.txt | awk '{print $1}'`
printf "chromosome $i, original_bam:$original, realigned_bam:$realigned, common:$same \n"
done
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