Hi,
I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.
--- samtools command ---
samtools mpileup -uf ref.fa sorted.bam | bcftools view -cg - | /usr/share/samtools/vcfutils.pl vcf2fq > conseqs.fastq
----
In IGV, I can create consensus sequence for all references (one by one). I would like to create the consensus sequences with a command line tool like samtools. Is there a way to make samtools to produce all consensus sequences like IGV does?
Thanks
I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.
--- samtools command ---
samtools mpileup -uf ref.fa sorted.bam | bcftools view -cg - | /usr/share/samtools/vcfutils.pl vcf2fq > conseqs.fastq
----
In IGV, I can create consensus sequence for all references (one by one). I would like to create the consensus sequences with a command line tool like samtools. Is there a way to make samtools to produce all consensus sequences like IGV does?
Thanks
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