Hi,
I am trying to run samtools mpileup on multiple bam files but for some reason I am getting the error "view: invalid option -- 'b'" and I end up with an empty bcf file.
This is my code:
samtools mpileup -uf ref.fa sample1_sorted.bam sample2_sorted.bam sample3_sorted.bam | bcftools view -bvcg - > group_var.raw.bcf
I have indexed the reference and all bam files using samtools and all files are in the same directory. Why would the b option be invalid? If I remove all bam files except one, the analysis works.
Thank you!
I am trying to run samtools mpileup on multiple bam files but for some reason I am getting the error "view: invalid option -- 'b'" and I end up with an empty bcf file.
This is my code:
samtools mpileup -uf ref.fa sample1_sorted.bam sample2_sorted.bam sample3_sorted.bam | bcftools view -bvcg - > group_var.raw.bcf
I have indexed the reference and all bam files using samtools and all files are in the same directory. Why would the b option be invalid? If I remove all bam files except one, the analysis works.
Thank you!
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