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 abundance of reads in my data. My problem is 1. The consensus file that I am getting is exactly similar to reference file. 2. For abundance of reads how should I use vcf file? Is there any way to convert vcf to fasta? Used 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 consensus.fa is same as reference.fa Thank You Regards Renuka Agarwal Graduate student IISER Mohali
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