README.md

Realignment

I used information from this article.

Install Dependencies

Picard:

git clone /~https://github.com/broadinstitute/picard.git
cd picard
./gradlew shadowJar

GATK 3.7:

wget https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.7-0-gcfedb67

Realignment Workflow

Execute first two steps only in case your BAM is malformed:

• Create Sequence Dictionary

java -jar picard/build/libs/picard.jar  CreateSequenceDictionary R=<name.fasta> O=<name.dict>

• Add or Replace Read Groups

java -jar picard/build/libs/picard.jar AddOrReplaceReadGroups I=<bam01.bam> O=<bam01_RG.bam> RGPL=illumina RGLB=lib1  RGPU=unit1  RGSM=2

• Create target intervals

java -jar GenomeAnalysisTK.jar  -T RealignerTargetCreator -R <file.fasta> -I <file.bam> -o <name.list>

• Realign reads

java -jar GenomeAnalysisTK.jar -T IndelRealigner -R <file.fasta> -I <file.bam> -targetIntervals <name.list> -o <file_realigned.bam>