README.md

Sample files to test shorah shotgun

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.