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Illumina / strelka

Strelka2 germline and somatic small variant caller
GNU General Public License v3.0
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Can't find any expected BAM/CRAM index files #200

Open MaitreyaSil opened 3 years ago

MaitreyaSil commented 3 years ago

Hi,

I am trying to run strelka germline workflow. However, everytime I run it throws the following error: configureStrelkaGermlineWorkflow.py: error: Can't find any expected BAM/CRAM index files for: '/path_to_file/filename.bam'. But, the said file exists on that given path. I also ran the demo file to check that strelka was installed properly. I will be glad if anyone can come up with a solution to this.

cheers, Maitreya

AlirezaDoustmohammadi commented 1 year ago

Hi Maitreya

To solve this error, you should do these steps:

  1. convert your SAM file to a BAM file & sort it using this command: samtools sort -@ 8 input.sam -o output.bam

  2. make an index file for your BAM file using the following command: samtools index output.bam

best, Alireza