haplotype_caller spark

haplotype_spark.sh

cd /data/samples/CORRIELL/mbi_cwiczenie3

### create sequence dictionary
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
broadinstitute/picard \
CreateSequenceDictionary \
R=/data/chr1.fa \
O=/data/chr1.dict

## validate BAM file
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
broadinstitute/picard \
ValidateSamFile \
I=/data/coriell_chr1.bam \
MODE=SUMMARY

# add @RG to BAM
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
broadinstitute/picard \
AddOrReplaceReadGroups \
I=/data/coriell_chr1.bam \
O=/data/coriell_chr1_rg.bam \
RGLB=lib1 \
RGPL=illumina \
RGPU=12 \
RGSM=1234

# validate again
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
broadinstitute/picard \
ValidateSamFile \
I=/data/coriell_chr1_rg.bam \
MODE=SUMMARY

#create index for BAM file
samtools index coriell_chr1_rg.bam

# run regular HC
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
broadinstitute/gatk \
gatk HaplotypeCaller \
 -R /data/chr1.fa \
 -I /data/coriell_chr1_rg.bam \
 -O /data/coriell_chr1.vcf.gz
 
# 13:23:12.145 INFO  ProgressMeter - Traversal complete. Processed 839864 total regions in 2.1 minutes.


# run HC on Spark (local)
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
broadinstitute/gatk \
gatk HaplotypeCallerSpark \
 -R /data/chr1.fa \
 -I /data/coriell_chr1_rg.bam \
 -O /data/coriell_chr1_spark.vcf.gz 
# [December 5, 2019 1:49:41 PM UTC] org.broadinstitute.hellbender.tools.HaplotypeCallerSpark done. Elapsed time: 2.49 minutes.

# run HC on Spark (YARN)
docker run --rm -it \
-v /data/samples/CORRIELL/mbi_cwiczenie3:/data \
-v $HADOOP_CONF_DIR:$HADOOP_CONF_DIR \
-e HADOOP_CONF_DIR=$HADOOP_CONF_DIR \
-v $SPARK_HOME:$SPARK_HOME \
-e SPARK_HOME=$SPARK_HOME \
broadinstitute/gatk \
gatk HaplotypeCallerSpark \
--spark-runner SPARK \
--spark-master yarn \
 --conf "spark.executor.memory=2g" \
 --conf "spark.driver.memory=2g" \
 --conf "spark.executor.instances=20" \
--conf "spark.hadoop.yarn.resourcemanager.address=192.168.157.201:8032" \
 -R /data/chr1.fa \
 -I /data/coriell_chr1_rg.bam \
 -O /data/coriell_chr1_spark.vcf.gz