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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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merge command collapsing non-identical variants to single record #2063

Open Logan-Wallace opened 8 months ago

Logan-Wallace commented 8 months ago

Hi there, When using the merge command to combine VCFs from 60 individuals I am getting an output which includes non-identical variants being output to the same record without a way for me to parse how the allelic ratios for each individual accord to the collapsed variant calls. For example, multiple duplication events output to the same record because they share the same start location but there isn't a way to tell to which variant the allelic ratio for a given individual accords. The argument --collapse none would seem to solve this problem but isn't available for the merge command. Is there a method to stop non-identical variants from outputting to the same record in the merged file or could the --collapse option be added to the merge command?

Command - bcftools merge –file-list vcf_filenames -Oz -o merged_files.vcf.gz

Screenshot 2023-12-21 at 11 35 59 AM
pd3 commented 8 months ago

How do you distinguish the duplications, by their ID? Would --merge id work in such case?