An error in running get-reads-alt-unmap.sh script

humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data

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An error in running get-reads-alt-unmap.sh script #10

Closed Yiming-Shen closed 7 years ago

Yiming-Shen commented 7 years ago

I tried to run get-reads-alt-unmap.sh script: ./get-reads-alt-unmap.sh my_file.bam processed.bam to pre-process a bam file but kept receiving error staring with: sambamba-view: Reference with name my_file.bam does not exist I was working in the directory where the bam file is in.

tanghaibao commented 7 years ago

@Yiming-Shen I tried to correct the sambamba command in the get-reads-alt-unmap.sh script. It should be ok now. Please let me know if you continue to have issues with it.

Haibao