Petr Danecek

Yes, that's correct. The quality is the phred score of the average fwd-bwd probability in the called region. Length and fragmentation of calls matters too. There is a plan to...

It should be possible to stream through `view` first? ``` bcftools view -i 'MAF

It would be nice to give more context, specifically which command produced this error message. I am guessing it's `bcftools call`? Your guess is correct, there are too many alternate...

Can you please post the command and the offending line?

BCFtools is a germline variant caller and assumes that the reads were sampled from a diploid genome. There are other variables entering the calculation, not just genotype likelihoods. Consider that...

The columns of the regions file can contain either positions (two-column format) or intervals (three-column format): CHROM, POS, and, optionally, END. In your file you requested the position 1 on...

@Bilvikakasturi The program does print the cause: it cannot parse the 1st line of the file (pardon the grammatical error of the error message, the code does not distinguish between...

The command `annotate` is intended for something else. I am not sure what you are trying to do. Merge the constituent SNVs back to a MNV, such as in the...

Thank you for this issue. As far as I remember, the sample IDs did not try to match the order of samples in the input file, but it is still...

The commands to download and compile are given above, including the download of the latest htslib. See here http://samtools.github.io/bcftools/howtos/install.html for more