Hi, I am working on variant calling with a fungal genome. When I am trying to reorder my .bam file (sorted) using picard ReorderSam (picard v2.9.0) to be used further in GATK realignment & BQSR, it throws this error:
Exception in thread "main" picard.PicardException: Discordant contig lengths: read scaffold1 LN=4751343, ref scaffold1 LN=4340956
Command I used,
java -jar /path/to/picard.jar ReorderSam I=myfile.bam O=reordered.bam R=myreference.fa
I checked my reference.fa file and found that the length of scaffold1 mention was incorrect (4751343), so I corrected it (LN=4340956) and created the .dict file again. But, I am still getting the same error.