adaptations for analyzing SARS-cov-2 sequencing data

b5c2df4a · ivanto · Susana Posada-Cespedes · c30b6f82 · b5c2df4a · c30b6f82
Commit b5c2df4a authored 4 years ago by ivanto 🦁 Committed by Susana Posada-Cespedes 4 years ago
--- a/references/NC_045512.2.fasta
+++ b/references/NC_045512.2.fasta
--- a/references/cohort_consensus.fasta
+++ b/references/cohort_consensus.fasta
--- a/references/cohort_consensus.fasta
+++ b/references/cohort_consensus.fasta
+NC_045512.2.fasta
\ No newline at end of file
--- a/vpipe.config
+++ b/vpipe.config
@@ -3,11 +3,13 @@ aligner = bwa

 [input]
 samples_file = samples.tsv
-reference = references/cohort_consensus.fasta
 fastq_suffix = 
+reference = references/NC_045512.2.fasta

 [output]
 snv = True
-local = False
+local = True
 global = False

+[hmm_align]
+leave_msa_temp = true