bcftools filetype error
I am trying to run this line:
bcftools mpileup -f $BT2_HOME/example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -Ov - > eg2.raw.bcf
When I do I get the following error:
[E::fai_build3_core] Failed to open the file /example/reference/lambda_virus.fa
Failed to read from standard input: unknown file type
This file, lambda_virus.fa, is the example file for using Bowtie2/samtools/bcftools and this is the code fro the Botwie2 manual. It adds the file eg2.raw.bcf to my folder but the file doesn't have any data it was just created blank. I am using bcftools version 1.14 on mac.
How can I fix this?
1 answer
the problem is -f $BT2_HOME/example/reference/lambda_virus.fa followed by the error message Failed to open the file /example/reference/lambda_virus.fa so your variable BT2_HOME is not defined or empty.
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