Petr Danecek comments

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                                            Petr Danecek

Feature Request: +setGT plugin ability to set GT in a subset of samples in the VCF file

I am wondering if `bcftools annotate` cannot be used for this task already?

Feature Request: +setGT plugin ability to set GT in a subset of samples in the VCF file

Yeah, there are so many features it's difficult to keep a track of them. Sometimes even for me :) From the perspective of the program, genotype is just another tag,...

could not parse the input VCF

That's very odd. What version of bcftools are you running, what is the output of ``` bcftools --version ```

could not parse the input VCF

Still very odd. In order to debug this, can you run ``` bcftools mpileup -f hg38.fa -o test.vcf -Ov $file ``` and share the output, possibly narrowing it down to...

could not parse the input VCF

Wow, 150GB? Usually the program works with very small memory requirements. I wonder what are your data like that require so much memory..

bcftools merge works but outputs a merged vcf with some of the genotypes prefixed with "/" e.g. /0|0, /0|1, /1|1 etc

This looks like a problem with the new prefixing of partially phased genotypes, likely introduced by https://github.com/samtools/htslib/commit/b14fffb4 I believe the intention was to explicitly prefix half-phased genotypes such as `/0/1|2`...