search

ssadedin / bazam

A read extraction and realignment tool for next generation sequencing data
GNU Lesser General Public License v2.1
99 stars 16 forks source link

how to run on CRAM #8

Closed brentp closed 6 years ago

brentp commented 6 years ago

when I run on cram I get an error message including:

Exception in thread "main" java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download

how/where can I set this from the command-line?

ssadedin commented 6 years ago

Bazam is using the underlying HTSJDK libraries, so you can inform it about how to locate the reference using the standard properties that HTSJDK supports. The most simple way is to directly specify it using the samjdk.reference_fasta property, eg:

java  -Xmx8g -Dsamjdk.reference_fasta=/reference/hg38/Homo_sapiens_assembly38.fasta -jar build/libs/bazam.jar test.cram > test.fastq.gz

Thanks for mentioning as this is not well documented!

brentp commented 6 years ago

thanks!

ssadedin commented 6 years ago

Closing now that this is documented in the main README.