Question: mpileup Error cannot open file type
gravatar for lewissechrome
3.5 years ago by
lewissechrome0 wrote:

Hi! I have been working with next-gen data for a few months now (no training) and I have been trying to develop vcf files from a BAM and FASTA file. On one set of data I found that this command worked well and produced the file and data I am looking for: samtools mpileup -uf Reference_slow_base_Slow_Cmac-32w.fa Cmac_L_S_A_baseline_slow_mapping.bam | bcftools call -cv > var.raw2.vcf

However when I swap in a different FASTA and BAM file (that are aligned to each other), I get errors like unknown file type or failed to load. I have tried indexing the FASTA and BAM files and running them with the index and it still comes back with errors. Any ideas?

sequencing alignment next-gen • 1.1k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 3.5 years ago by lewissechrome0
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