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Questions tagged [bcftools]

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2
votes
2answers
66 views

extracting last few lines of a growing bgzip compressed .vcf.gz file

I am running bcftools merge to create a single .vcf.gz file out of a collection of chromosomal ...
4
votes
3answers
596 views

How to get fasta alignment file from SAM/BAM file?

I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's ...
5
votes
3answers
132 views

bcftools filtering all files in a directory

Probably a silly oversight on my part, but I'm trying to filter all the vcfs in a directory with bcftools using a simple loop. My basic command is working fine: ...