bwa 설치 및 명령어

bowtie

1. 다운로드

1) https://sourceforge.net/projects/bio-bwa/?source=typ_redirect

2) 적절한 버전을 선택한다.

2. 압축을 푼다(unzip)

tar jxf bwa-0.6.2.tar.bz2

3. make와 make install실행

make

make install

4. path설정

export PATH=$PATH:/mnt/tools/bwa-0.6.2

진하게 쓴 부분은 bwa의 경로를 설정하면 된다.

5. /usr/local/bin 으로 bwa를 cp해서 옮긴다.

cp /path/to/bwa /usr/local/bin/bwa

6. reference genome 다운로드 받기 및 

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

tar zvfx chromFa.tar.gz

7. 개별 chromosome reference fa를 하나로 묶어줌

cat *.fa > wholegenome.fa

8. wholegenome fasta파일을 indexing하기- 이건 한번만 하면 됩니다.

bwa index -p hg19bwaidx -a bwtsw wholegenome.fa

where -a bwtsw specifies that we want to use the indexing algorithm that is capable of handling the whole human genome.

8A. samtools faidx wholegenome.fa

This creates a file called reference.fa.fai, with one record per line for each of the contigs in the FASTA reference file.

9. Paired-Read align하는 명령어

각각 개별적으로 돌려주고 하나로 해줘야함.

bwa aln -t 4 hg19bwaidx s_3_1_sequence.txt.gz >  s_3_1_sequence.txt.bwa
bwa aln -t 4 hg19bwaidx s_3_2_sequence.txt.gz >  s_3_2_sequence.txt.bwa
bwa sampe -r '@RG\tID:yuhs\tSM:KNS81' hg19bwaidx s_3_1_sequence.txt.bwa s_3_2_sequence.txt.bwa s_3_1_sequence.txt.gz s_3_2_sequence.txt.gz > s_3_sequence.txt.sam

-r이란 옵션은 header를 만들어주는 것인데 이게 없으면 picard가 안돌아감.

참고

http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial

http://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups