Simulates a reference and some reads. The reads have a 15bp insertion relative to the reference, and 1 SNV.
Uses standard bioinformatic tools to align the reads, call the variants, and produce a consensus sequence. The consensus should differ from the reference at exactly the single SNV, and the 15bp insertion.
To run, just call make
. For more control, targets can be made in order (each step will also make its prerequisites):
make simulation
: just make the simulated reference and readsmake alignment
: run bwa mem to align the reads to the referencemake pileup
: run bcftools mpileup on the simulated readsmake calls
: run bcftools call on the pileup resultmake filtered
: run bcftools filter on the calls to consolidate overlapping indelsmake consensus
(equivalent tomake all
): run bcftools consensus on the callsmake clean
: clean up all generated files
Outputs (not including various indexing files):
ref.fa
: simulated reference sequencereads.fq
: simulated reference readsaln.bam
: reads aligned to referencepileup.vcf
: pileup resultcalls.vcf
: calls obtained from pileupcalls.bcf
: filtered calls obtained from pileupconsensus.fa
: consensus sequence
Comparing consensus.fa
to ref.fa
shows the 15bp insertion.