Error in reordering a bam file

nghiavtr / SCmut

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Error in reordering a bam file #5

Open dzy-3737 opened 4 years ago

dzy-3737 commented 4 years ago

Hi,

I'm used the SCmut to analyze my scRNA datasets. However, when i try to reordering a bam file a error happen and the statement are as follows:

my code : java -Xmx16g -Djava.io.tmpdir=pwd/tmp -jar /home/dzy/picard.jar ReorderSam VALIDATION_STRINGENCY=SILENT I=$readgroup_fn O=$reorder_fn R=$genomeFasta_b37

ERROR: Option 'SEQUENCE_DICTIONARY' is required.

I'll appreciate it if you can help me to solve the problem.

nghiavtr commented 4 years ago

Hi @dzy-3737,

Thank you for using SCmut.

I used picard version 2.3.0 for analyses but have not seen this error before. Which picard version are you using? Might be other versions of picard have some slight changes in the input parameters.

Best, Nghia

Triqueon commented 3 years ago

In Case anyone stumbles across this, evidently in newer versions of Picard, the R or REFERENCE option was changed to be called SEQUENCE_DICTIONARY. Also, you will have to use Picard to create a sequence dictionary from the fasta file before this will work.

nghiavtr commented 3 years ago

@Triqueon Thank you for your suggestion.

Best, Nghia