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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.
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