Elementolab/CNVseeqer

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Installation

svn checkout https://pbtech-vc.med.cornell.edu/public/svn/elementolab/CNVseeqer/trunk CNVseeqer/
cd CNVseeqer
export CNVSEEQERDIR=`pwd`   # better: add export CNVSEEQERDIR=/path/to/CNVseeqer to .bashrc (replace /path/to by a real path)
# BIO-C is needed ... if ls ../BIO-C does not work, than it is not installed
make
# scripts also need GD::Simple Perl module
# one possibility:
# sudo perl -MCPAN -e shell
# install GD::Simple

Tutorial

Step 1: make BAM files

bwa sampe /home/yaj2001/work2/SNPseeqer/hg19bwaidx s_1_1_sequence.txt.gz.hg19.bwa  s_1_2_sequence.txt.gz.hg19.bwa s_1_1_sequence.txt.gz s_1_2_sequence.txt.gz > s_1_sequence.txt.sam
samtools view -bS s_1_sequence.txt.sam > s_1_sequence.txt.bam
samtools sort s_1_sequence.txt.bam s_1_sequence.txt.sorted    # will create s_1_sequence.txt.sorted.bam
bwa sampe /home/yaj2001/work2/SNPseeqer/hg19bwaidx s_2_1_sequence.txt.gz.hg19.bwa  s_2_2_sequence.txt.gz.hg19.bwa s_2_1_sequence.txt.gz s_2_2_sequence.txt.gz > s_2_sequence.txt.sam && sam2sbam s_2_sequence.txt.sam
samtools view -bS s_2_sequence.txt.sam > s_2_sequence.txt.bam
samtools sort s_2_sequence.txt.bam s_2_sequence.txt.sorted    # will create s_2_sequence.txt.sorted.bam

Step 2: find CNVs

 ./CNVseeqer -chrdata REFDATA/hg19.chrdata -bamfile1 s_1_sequence.txt.sorted.bam -bamfile2 s_1_sequence.txt.sorted.bam -captured SureSelect_All_Exon_50Mb_hg19.txt -verbose 1 -outfile exoncnv.txt 

Step 3:

 perl DrawCNVMapMultiChromosomes.pl --exondata=exoncnv.txt --chrdata=REFDATA/hg19.chrdata 
 (will create exoncnv.txt.png)
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