Problem calling somatic variations using Strelka-2 (configureStrelkaSomaticWorkflow.py)
Hi I am trying to call somatic variations using Strelka2, but I get this error:
configureStrelkaSomaticWorkflow.py Can't find expected fasta index file: index_bwa/hg38.fa.fai
I'm doing the exact command given from the website:
strelka-2.9.2.centos6_x86_64/bin/configureStrelkaSomaticWorkflow.py --normalBam BC.bam --tumorBam XL.bam --ref index_bwa/hg38.fa --runDir demo_somatic
I got this command from the recommended workflow of the website (Link).
Any help? Thanks!
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Fasta index file is missing. Index fasta file. Navigate to index_bwa folder, execute
samtools faidx hg38.faand then execute strelka functions.Should move that to answer.
Thank you
I applied your suggestion but now the error changed to this one:
I tried with sorted.bam as well, but got the same error.
Any help?
Just read the error message, it explicitly tells you what's wrong.
this error is regarding index file missing for BC.bam. Index both the bams.
samtools index <input.bam>.Hello R.A.!
We believe that this post does not fit the main topic of this site.
Same issue as with your VarScan question. Index files are missing.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!