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
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