I am running ReorderSam to try and match my bam files to the order of the reference but it looks like they are in the same order, but somehow the reference (Mus_musculus.GRCm38.dna.primary_assembly.dict)
is lacking the contig ERCC-00002. Because of this issue I cannot proceed with my pipeline (SplitNCigarReads fails)
My code is:
for fn in $(find /home/colpe/scratch/raw_data/marked_dup/ -name "*.bam")
gatk ReorderSam -I "$fn" -O /home/colpe/scratch/raw_data/marked_reordered/"$(basename $fn)"_reordered.bam -SD /home/colpe/data/ref_sequences/Mus_musculus.GRCm38.dna.primary_assembly.dict
The error I get is:
picard.PicardException: New reference sequence does not contain a matching contig for ERCC-00002
Should I just remove this contig from my bam files?
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