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Variant discovery on bwa data using GATK

Once again we need to add the read groups to the mapped bam file.

java -jar AddOrReplaceReadGroups.jar I=bwa.sorted.bam O=bwa_final.bam SORT_ORDER=coordinate RGPU=na RGID=1 RGLB=input RGPL=Illumina RGSM=Company CREATE_INDEX=True

We can then go on and run GATK as before, but using the revised bam file.

java -jar GenomeAnalysisTK.jar \
-R chr17.fa \
-T HaplotypeCaller \
-I bwa_final.bam \
-L chr17:41,196,311-41,277,499 \
-o bwa_snps.vcf

And check the output as before:

grep -v "^#" bwa_snps.vcf | wc -l