Use files in this directory to test shorah in shotgun mode.
The reads data comes from the
test-data
of V-pipe
and has been processed with the pipeline using the bwa
option:
[general]
aligner = bwa
The sorted bam file has been further compressed with samtools for space saving:
[user@host shotgun_test]$ samtools view -T test_ref.fasta -C -O cram,embed_ref,use_bzip2,use_lzma,level=9,seqs_per_slice=1000000 -o test_aln.cram V-pipe/work/samples/2VM-sim/20170904/alignments/REF_aln.bam
You can then run shorah shotgun
as follows
[user@host shotgun_test]$ shorah shotgun -b test_aln.cram -f test_ref.fasta
The output files will be snv/SNVs_0.010000_final.vcf
and snv/SNVs_0.010000_final.csv
.