Questions tagged [bcftools]

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Bcftools call always assigns a genotype even if there are no reads?

I am variantcalling my 96 multi sampled bam file with samtools/bcftools however I obtain some strange results. When I use the following command: ...
1
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1answer
24 views

How to do the reverse of bcf merge?

How can one do the reverse of bcftools merge? To get one sample back out of the merged one. Without holding reference sites.
2
votes
2answers
130 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
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3answers
925 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
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3answers
153 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: ...