Greetings,
I'm trying to pull out a region of a consensus using the recommended flow:
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - |
vcfutils.pl vcf2fq > cns.fq
When I limit this to a region in samtools mpileup, vcfutils will place Ns
from the first position in the chromosome to the position with data. Is
there a way to change that in the script so only positions with data (or in
a region) have reported values?
For example:
samtools mpileup -r NC_012312.1:5,474-7,015
-uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
There will be 5474 Ns in the fastq file cns.fq prior to the first base with
data.
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