Pierre Lindenbaum
"constrained trio calling temporarily disabled"
https://github.com/samtools/bcftools/blob/develop/mcall.c#L1605C30-L1605C75
bcftools 1.23 released https://github.com/samtools/bcftools/releases/tag/1.23
Luke PembletonMaybe I need another coffee, but is there anyway to tell #bcftools what ALT allele to add to the ALT column of a called vcf even if it wasn't observed in the read data (instead of '.') i.e. a known ALT allele from another larger dataset?
#bioinformatics
#bioinformatics
So after much community backlash #GATK has reverted back to the ./. representation for no-calls.
The question is, will something like this occur again? and how many people have already switched away to other tools like #bcftools.
I know I have moved all my pipelines back to bcftools and honestly its brilliant.
What’s everyone’s thoughts and experience on merging large numbers of gvcf files? Currently I’m running #bcftools merge, but as a tree merge process (multiple smaller merges that then get merged together). I’ve seen there is #IMMerge which is meant to have speed improvements. Are there any other tools or hacks people are using? 🧬
Hey 👋 I was wondering if anything had any insight into what I am observing here in a #VCF file produce from #bcftools.
It's very low coverage (i.e. 1 read) as it is some trimmed down test data for a pipeline. Even so while the DP at these positions is 1, and upon inspection in IGV the read base is an alternative allele (also indicated in the DP4 field), the AD field ignores it and in the end it is called as homozygous reference 🤔
#bioinformatics #genomics
It's very low coverage (i.e. 1 read) as it is some trimmed down test data for a pipeline. Even so while the DP at these positions is 1, and upon inspection in IGV the read base is an alternative allele (also indicated in the DP4 field), the AD field ignores it and in the end it is called as homozygous reference 🤔
#bioinformatics #genomics
G’day legends, if you are looking to just simply extract a subset of SNP positions from a VCF, bcftools -T (targets) is, by my own account, 3X faster than -R (regions). So unless you enjoy having a staring 👀 contest with your terminal, I suggest using it.
Now, before anyone jumps on the no no train 🚂 obviously, there are other functionality differences between targets & regions, but for this scenario, it does the job 👍
PR accepted ! option "--drop-genotypes" in #bcftools concat https://github.com/samtools/bcftools/pull/1911 🥳🥳
