Use files in this directory to test shorah in amplicon mode.
The sorted bam file has been obtained from the reads with
smalt
to align reads to the reference and samtools to index and
sort the alignment. The commands given are
[user@host amplicon_test]$ smalt index -k 7 -s 2 ref reference.fasta
[user@host amplicon_test]$ smalt map -f sam -o ampli.sam ref amplicon_reads.fastq
[user@host amplicon_test]$ samtools view -S -b ampli.sam | samtools sort - ampli_sorted
You can then run shorah amplicon as follows
[user@host amplicon_test]$ shorah amplicon -b ampli_sorted.bam -f reference.fasta
Some warning will be raised. The output files will be SNV.txt and SNVs_0.010000_final.csv.
Only SNVs exceeding the threshold of 5% are returned (see paper).
You can inspect the alignment with samtools tview:
[user@host amplicon_test]$ samtools index ampli_sorted.bam
[user@host amplicon_test]$ samtools tview ampli_sorted.bam reference.fasta
Within tview, press ? for help.
shorah amplicon is still under development.