I'm working on RNA-seq data and have aligned my reads to the assembled transcript using bwa-mem. When I tried to run Picard Tools (SamFormatConverter.jar), the SAM dictionary threw an exception "Cannot add sequence that already exists in SAMSequenceDictionary".
I then checked for duplication in the SAM file header and sure enough, two entries were duplicated. How do I correct this? Commands used are given below:
bwa index contigs.fa bwa mem contigs.fa reads_1.fq reads_2.fq >samFile.sam java -Xmx4g -jar SamFormatConverter.jar INPUT=samFile.sam OUTPUT=bamFile.bam
This is where I faced the error.
I checked for duplicates using:
samtools view -HS samFile.sam | sort | uniq -c
2 @SQ entries were present >1 times.
Any help would be appreciated, thanks!