Hi
I have started using samtools and bcftools for the analysis of microbiome
data generated by oxford nanopore minion. After aligning the file using
LAST tool, I am using samtools. I have sorted bam file for my data, now
want to do variant calling and make consensus file. My aim is to see the
abund
Hi,
I'd like to help, but I don't understand what the problem is.
The `bcftools mpileup .. | bcftools call` command calls variants,
`bcftools consensus` then creates a fasta consensus sequence.
Please read the documentation.
http://samtools.github.io/bcftools/howtos/consensus-sequence.html
http
Hi,
I don't see anything obviously wrong in your commands. Take a look in
calls.vcf.gz, are there any variants?
Here is a brief documentation, maybe it will give some useful pointers
http://samtools.github.io/bcftools/howtos/consensus-sequence.html
http://samtools.github.io/bcftools/howtos/varia
Hi
I am using samtools and bcftools to generate consensus sequences for my
microbiome data. After generating sorted bam file from samtools, I used
mpileup command of bcftools.
Commands were
bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call
-mv -Oz -o calls.vcf.gz
bcftools index c
