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/variant-calling.html Best wishes, Petr On Tue, 2019-02-12 at 05:09 +0530, Renuka Agarwal wrote: > 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 calls.vcf.gz > Then for making consensus I used > bcftools consensus -f reference.fa calls.vcf.gz > consensus.fa > But the file that is being produced is actually my database file, > i.e., reference.fa= consensus.fa > Can anyone help why is it happening and what is sample file (-s), how > can i get that. > Thank you! > > Regards > Renuka Agarwal > PhD Scholar > IISER Mohali > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforg > e.net_lists_listinfo_samtools- > 2Dhelp&d=DwICAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=xdvdT > aAZDWitAtUqWIZL0A&m=Ujv3HP7kyuPZTvvZxIU2n_snvGkskBB_Mgy_bFA6FgE&s=bEY > e8OcktUAq8FZ0zP1WZf40XwhB49ece4bs5IuZ9G8&e= -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
