Petr Danecek
Petr Danecek
I don't understand this well. The VCF fragment you're showing ``` chrX 31709584 ./. 0/1 ./. 0/0 chrX 31709584 ./. 0/0 ./. 0/1 chrX 31709584 . . 1 . ```...
Hopefully this should fix it. Although still not sure how one would end up with a mixture of different ploidies.
Changing BCF specification is not an easy task and may take a long time even if there is a good will to do it. The problem could be addressed more...
Yes, that is correct, one must compile with -DVCF_ALLOW_INT64. Try to force recompilation of vcf.c with `touch vcf.c`, see what the standard `make` command line looks like and add -DVCF_ALLOW_INT64....
There is the plugin `+fill-tags` which can calculate FORMAT/VAF from FORMAT/AD, then one can filter on VAF using the `-i/-e` filtering expressions http://samtools.github.io/bcftools/bcftools.html#expressions
Depending on the version used, recent versions of mpileup have to be run with `-a INFO/FS` in order for the field to be populated. Run `bcftools mpileup -a \?` to...
It's a tab-delimtied file with the columns `chrom`, `pos` and optional `end`. This is described in the manual page http://samtools.github.io/bcftools/bcftools.html
Please share a small test case to for us verify what's going on. What you show looks correct on a cursory glance.
> I am using 91 bam files each of 500 mb size Bam files sorted and indexed and reference maize genome is also indexed of 2.5 gb . Then i...
Mmm, the attempted fix does not work universally, `isatty` does not work as expected on some systems.