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Name Modified Size InfoDownloads / Week
README1.2.txt 2017-08-24 1.0 kB
physical_depth_chimeric 2017-08-24 6.0 MB
samechr.sh 2017-08-24 1.1 kB
difchr.sh 2017-08-24 1.1 kB
check_difchr_cluster 2017-08-24 6.0 MB
check_samechr_cluster 2017-08-24 6.0 MB
BCA.tar.gz 2017-07-25 195.0 MB
README.txt 2017-07-25 1.0 kB
Totals: 8 Items   213.1 MB 0
Updated files include:
./physical_depth_chimeric ###################include the classification of whether -M option was set when BWA mem alignment was performed
./CRA/check_difchr_cluster 
./CRA/check_samechr_cluster 
./CRA/Difchr/difchr.sh	
./CRA/Samechr/samechr.sh	
#############The other four programs/shells/ include insert size to classify the small-insert or mate-pair library as they have different orientations of alignment

##############################Please put these programs/shells into the certain paths to replace the older ones before running the whole pipeline#####################


Command line revised as below:
Step1. ./physical_depth_chimeric ./BAM ./difchr.gz ./samechr.gz <alignment method: aln or mem> <M|N: -M option for mem> <path for samtools (use absolute address)>

Step5. sh ./CRA/Difchr/difchr.sh ./difchr.fil.sort.final.gz <sample ID> <ethnic pop:AFR,AMR,ASN,EUR,SAN> <500|5000>

Step6. sh ./CRA/Samechr/samechr.sh ./samechr.fil.sort.final.gz <sample ID> <ethnic pop:AFR,AMR,ASN,EUR,SAN> <500|5000>
Source: README1.2.txt, updated 2017-08-24