Hello,
I am trying to follow the simple tutorial (
http://samtools.sourceforge.net/mpileup.shtml) to call variants with
samtools.
I am actually having trouble at the first command "samtools mpileup
-uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
".
I try:
@NCS ~/samtools_diploid $ samtools mpileup -uf gdr18_k75-85_NHC_conc.fasta
../../GDR-18.sort.grp.md.bam | bcftools view -bvcg - >
GDR-18.raw.bcf
view: invalid option -- 'b'
...
If I remove "-b" I get:
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[E::cg] unknown type
Anyone have any advice on how I can simplify this?
Thank you,
Adrian
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