how to set R parameter in MergeBamAlignment in Picard

Question

[Yingzi Zhang]

Dear all, I am trying to use picard MergeBamAlignment to prepare files for GATK. I know the usage should be

java -jar picard.jar MergeBamAlignment \
ALIGNED=aligned.bam \
UNMAPPED=unmapped.bam \
O=merge_alignments.bam \
R=reference_sequence.fasta

Actually I wrote so. But it reported that

SAMException: Could not find dictionary next to reference file file://<reference_sequence.fasta>

Why should this happened please? It could recognized my reference sequence file because there was

REFERENCE_SEQUENCE=reference_sequence.fasta

in the report. Is there any index I need to built? Thank you.

Yingzi

Answer 1

[ATpoint]

Yes, you have to build a reference dictionary. Google will provide you with details.

[Yingzi Zhang]

Got it. Thanks a lot.