##	Copy .bw files
for k in `cat  /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/analysis_by_chemical/gtx/BROMODICHLOROACETIC-ACID-_BDCA/BROMODICHLOROACETIC-ACID-_BDCA_samples.txt `;  do echo $k;  ls /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/mergedData/$k/customTrack/$k".bw"  ; done; 

for k in `cat  /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/analysis_by_chemical/gtx/BROMODICHLOROACETIC-ACID-_BDCA/BROMODICHLOROACETIC-ACID-_BDCA_samples.txt `;  do echo $k;  cp /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/mergedData/$k/customTrack/$k".bw" /data/wade/jianying/ArunExomeSeq/trackHubs/exomeHCCHubs/gtxBDCA/mm10/DATA/  ; done; 


##	Copy .vcf files

##	Centralized the variant call with PON etc!!!


#for k in `cat /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/analysis_by_chemical/gtx/BROMODICHLOROACETIC-ACID-_BDCA/BROMODICHLOROACETIC-ACID-_BDCA_samples.txt `;  do  cp /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/mergedData/$k/varCallDir/$k"_mutect_against_MaleNormal.vcf" /data/wade/jianying/ArunExomeSeq/trackHubs/exomeHCCHubs/gtxBDCA/mm10/DATA/  ; done;  

#for k in `cat /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/analysis_by_chemical/gtx/BROMODICHLOROACETIC-ACID-_BDCA/BROMODICHLOROACETIC-ACID-_BDCA_samples.txt `;  do cp  /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/mergedData/$k/varCallDir/$k"_mutect2_PON_w_BQSR_filtered.vcf"  /data/wade/jianying/ArunExomeSeq/trackHubs/exomeHCCHubs/gtxBDCA/mm10/DATA/   ; done;  



##	Create .gz and .tbi files 
#for k in `cat   /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/analysis_by_chemical/gtx/BROMODICHLOROACETIC-ACID-_BDCA/BROMODICHLOROACETIC-ACID-_BDCA_samples.txt `;  do bgzip /data/wade/jianying/ArunExomeSeq/trackHubs/exomeHCCHubs/gtxBDCA/mm10/DATA/$k"_mutect2_PON_w_BQSR_filtered.vcf"  ; done;  

#for k in `cat   /ddn/gs1/home/li11/project2018/NTP_exome_project/ReAnalyzeEffort/analysis_by_chemical/gtx/BROMODICHLOROACETIC-ACID-_BDCA/BROMODICHLOROACETIC-ACID-_BDCA_samples.txt`;  do tabix /data/wade/jianying/ArunExomeSeq/trackHubs/exomeHCCHubs/gtxBDCA/mm10/DATA/$k"_mutect2_PON_w_BQSR_filtered.vcf.gz"  ; done;