Question: Small number of reads mapping to consensus
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3.5 years ago by
stolarek.ir0 wrote:

Hi all,

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 vcf2fq -d 2 > cns.fq

The realigned my mapped reads to the called consensus, however now only 23% of them mapped.


Why is that?

alignment mtdna • 768 views
ADD COMMENTlink modified 3.5 years ago by Hotz, Hans-Rudolf1.8k • written 3.5 years ago by stolarek.ir0
gravatar for Hotz, Hans-Rudolf
3.5 years ago by
Hotz, Hans-Rudolf1.8k wrote:


This is not really a Galaxy related question, is-it? and you probably better ask this question at or

I am not really familiar with 'samtools mpileup' and 'bcftools', but I am guessing you are running into similar issues as with de-novo assembly, when you use too many reads as input.




ADD COMMENTlink written 3.5 years ago by Hotz, Hans-Rudolf1.8k
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