Samtools
Create output directory.
mkdir -p 03_Output/variant_calling/samtools
Preparing alignment file.
If you do not have a alignment file in the SAM format you may want to start with Introduction to mapping.
samtools view -bS -o 03_Output/variant_calling/samtools/REL606.5.bam 03_Output/mapping/bowtie/REL606.5.sam
[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "03_Output/mapping/bowtie/REL606.5.sam".
