Question: Small number of reads mapping to consensus
3.5 years ago by
stolarek.ir • 0
stolarek.ir • 0 wrote:
I aligned my single-end illumina reads with bwa aln to the human mitochondrial reference.
Then took only aligned reads and called consensus with:
samtools mpileup -uf mt_dna.fa mt_sorted.bam | bcftools view -cg - | perl vcfutils.pl vcf2fq -d 2 > cns.fq
The realigned my mapped reads to the called consensus, however now only 23% of them mapped.
Why is that?
ADD COMMENT • link •modified 3.5 years ago by Hotz, Hans-Rudolf • 1.8k • written 3.5 years ago by stolarek.ir • 0