Question: Samtools mpileup refrence fasta file input
0
gravatar for cvu
4.8 years ago by
cvu130
India
cvu130 wrote:

I'm using Samtools mpileup to convert my sorted.bam file to .bcf files. i've used multiple refrences to align my paired end reads. I've used GRCh38_Chr1 and GRCh38_Chr10.

samtools mpileup -g -f ref.fna aligned.sorted.bam > sim_variants.bcf

In above argument, how do i mention multiple reference fasta files ?

alignment snp next-gen assembly • 1.8k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 4.8 years ago by cvu130
2
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Just concatenate the files and use that.

ADD COMMENTlink written 4.8 years ago by Devon Ryan89k

okay . thanks Devon Ryan !!

ADD REPLYlink written 4.8 years ago by cvu130
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