Petr Danecek
Petr Danecek
Uh, the functionality of `--indels-2.0` relies heavily on the reference genome, at the moment it cannot work without it.
There are two read subsetting steps. First, the `mpileup -d` option controls the maximum number of reads in the pileup. Unfortunately, this is not random, the buffer fills up to...
Unfortunately, the `vcfutils.pl` script is no longer supported. I'll accept a pull request if anyone cares to fix it. Just to cross link, this is a duplicate of #1811 and...
This is a peculiar case. Any chance you could provide a test case to reproduce the error?
Please check the manual page and the howtos to get more familiar with the program http://samtools.github.io/bcftools/bcftools.html http://samtools.github.io/bcftools/howtos/index.html Regarding the ploidy, you can review the VCF header and see if there...
Thank you for the issue. Is there any chance you could provide a small test case to reproduce the error?
Any chances you could send the debugging output from valgrind?
Could you perhaps use this script to create a small slice of the bam and the reference https://github.com/pd3/mpileup-tests/blob/main/misc/create-bam-test, as in #2189? The script creates a short artificial chromosome, removes all...
This is a can of worms I hesitate to open. What is the minimal functionality that would address most of the problems? Converting all explicit indels into symbolic representation is...
The problem is we can't do `norm --symbolic-to-explicit` for insertions. That's part of my hesitation - would it be worth it