Samtools
Setup output directory.
mkdir -p 03_Output/variant_calling/samtools
If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
cp 03_Output/mapping/bowtie/REL606.5.sam 03_Output/variant_calling/samtools/
cp 03_Output/mapping/bowtie/REL606.5.fasta 03_Output/variant_calling/samtools/
Prepare reference file.
samtools faidx 03_Output/variant_calling/samtools/REL606.5.fasta
Prepare alignment file.
Convert SAM to BAM format.
samtools view -bS -o 03_Output/variant_calling/samtools/REL606.5.bam 03_Output/mapping/bowtie/REL606.5.sam
[samopen] SAM header is present: 1 sequences.
Sort BAM file.
samtools sort 03_Output/variant_calling/samtools/REL606.5.bam 03_Output/variant_calling/samtools/sorted_REL606.5
[bam_sort_core] merging from 2 files...
Variant call output.
samtools mpileup -uf 03_Output/variant_calling/samtools/REL606.5.fasta 03_Output/variant_calling/samtools/REL606.5.bam
[mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 [bam_pileup_core] the input is not sorted (reads out of order) [afs] 0:0.000 1:0.000 2:0.000 [bam_plp_destroy] memory leak: 1. Continue anyway.
