1718054  echo "/projects/rcorbettAlignment/NBL01/HS1780/30_lanes.rmdup.pileup.varFilter
1718055  /projects/rcorbettAlignment/NBL02/HS1781/29_lanes.rmdup.pileup.varFilter
1718056  /projects/rcorbettAlignment/NBL03/HS1782/30_lanes.rmdup.pileup.varFilter
1718057  /projects/rcorbettAlignment/NBL04/HS1783/31_lanes.rmdup.pileup.varFilter
1718058  /projects/rcorbettAlignment/NBL05/HS1784/30_lanes.rmdup.pileup.varFilter
1718059  /projects/rcorbettAlignment/NBL06/HS1794/25_lanes.rmdup.pileup.varFilter
1718060  /projects/rcorbettAlignment/NBL07/HS1796/29_lanes.rmdup.pileup.varFilter
1718061  /projects/rcorbettAlignment/NBL08/HS1798/25_lanes.rmdup.pileup.varFilter
1718062  /projects/rcorbettAlignment/NBL09/HS1800/26_lanes.rmdup.pileup.varFilter
1718063  /projects/rcorbettAlignment/NBL10/HS1802/25_lanes.rmdup.pileup.varFilter
1718064  /projects/rcorbettAlignment/NBL01G/HS1599/26_lanes.rmdup.pileup.varFilter
1718065  /projects/rcorbettAlignment/NBL02G/HS1600/28_lanes.rmdup.pileup.varFilter
1718066  /projects/rcorbettAlignment/NBL04G/HS1602/28_lanes.rmdup.pileup.varFilter
1718067  /projects/rcorbettAlignment/NBL05G/HS1603/25_lanes.rmdup.pileup.varFilter
1718068  /projects/rcorbettAlignment/NBL03G/HS1601/25_lanes.rmdup.pileup.varFilter
1718069  /projects/rcorbettAlignment/NBL06G/HS1884/21_lanes.rmdup.pileup.varFilter
1718070  /projects/rcorbettAlignment/NBL07G/HS1885/21_lanes.rmdup.pileup.varFilter
1718071  /projects/rcorbettAlignment/NBL08G/HS1886/21_lanes.rmdup.pileup.varFilter
1718072  /projects/rcorbettAlignment/NBL09G/HS1887/21_lanes.rmdup.pileup.varFilter
1718073  /projects/rcorbettAlignment/NBL10G/HS1888/22_lanes.rmdup.pileup.varFilter" | awk -F "/" '{ printf "ln -s %s %s_%s\n", $0, $4, $NF }'  | bash

ls *varFilter | xargs -i echo "cat {} | awk '{ print \$1,\$2,\$2,\$0 }' > {}.clean" | bash
cat all.exons.clean.txt.splice | sort -u +0 -3 > all.exons.clean.txt.splice.unique
cat all.exons.clean.txt.splice.unique | grep -v unspliced > all.exons.clean.txt.splice.unique.spliced
/home/rcorbett/lymphoma/tools/overlapcoordinates_ultrafast.pl -ref NBL.*clean -coord all.exons.clean.txt.splice.unique.spliced -dir /projects/NBL/snp_splice_sites
 join -1 2 -2 2 -v 1 NBL01_30_lanes.rmdup.pileup.varFilter.clean_ovlp.jsort NBL01G_26_lanes.rmdup.pileup.varFilter.clean_ovlp.jsort > NBL01.somatic
cat *somatic | c2 | sort | uniq -c | shrinkwrap > somatic_counts.txt
 ls *somatic | xargs -i echo "join -1 2 -2 1 somatic_counts.txt {} | cut -d ' ' -f 2- > {}.counts" | bash
ls *somatic.counts | xargs -i echo "awk '{ print \$2,\$3,\$3,\$1,\$0 }' {} | cut -d ' ' -f 1-4,10- > {}.clean" | bash