Samtools mpileup refrence fasta file input
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 ?
1 answer
Just concatenate the files and use that.
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Devon Ryan
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