Make a fasta out of mapped reads without taking into account the reference I've aligned reads onto an haploid reference genome. I'd like to have a consensus sequence of all my aligned reads that doesn't take into account the reference genome I used (i.e. I just want the nucleotides from my reads at each base (taking into account frequency and quality) but if there is no read a one position I rather have N/? than the reference nucleotide. 
Is there a way to do this ? Thanks
vSNP outputs a VCF file that includes positions with no coverage, represented as "N".  Then there is a tool to merge a VCF file into the FASTA reference  vsnp_merge_vcf_into_fasta.py.  It will merge those "N" regions into the FASTA reference. There are options for considering frequency and quality.
 It's limited to just SNPs and those regions along the reference with no coverage.  It does not merge small indels or unmapped reads.  Pilon is a better tool for applying indels, but I'm not aware of it letting regions with no coverage be represented as "N".

vSNP_step1.py -r1 *_R1*fastq.gz -r2 *_R2*fastq.gz -r ref.fasta


Use *zc.vcf output to merge into FASTA

vsnp_merge_vcf_into_fasta.py -f ref.fasta -v *_zc.vcf