.phased not correct for VCFs containing phased & unphased genotypes.

[rollf]

Hi,

I have a VCF that was processed with HiPhase. The file contains lines with "|" as well as "/" for the GT value. Example:

chrX	1189233	.	T	A	7.4	PASS	.	GT:GQ:DP:AD:VAF:PL:PS	0|1:7:4:1,3:0.75:6,0,19:1189207
chrX	1189258	.	G	A	30.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:13:4:0,4:1:30,12,0

nft-vcf incorrectly assumes that the file is not phased. Looking into the code I realize that a single slash in any line is sufficient to set phased to false (it's true by default and gets updated when reading the file). I rather think it should be the other way around: A single pipe ("|") should be sufficient to assume the VCF is phased (and set phased to false by default) - assuming the code stays roughly as is.

Further thoughts: The VCF 4.2 spec says that a PS field should be added for phased variants. Maybe one could check for this field instead of looping over the variants. The current approach assumes that a single unphased genotype means the whole VCF is unphased. That seems too strict (or even wrong). If the phasing information is something that is expected to change on a per-variant base, you might rather want to have a phased boolean array with a value for each variant.

[seppinho]

Thank you for bringing this up! In our primary use case (genotype imputation from microarray data), a single pipe isn’t sufficient to ensure the file is correctly phased. However, I agree that supporting a single-pipe configuration could be useful for other workflows.

If you’re interested, we’d love to see a Pull Request (PR) from you to implement this feature. My suggestion would be to add a new parameter to the load function to handle an alternative strategy.

See here:

nft-vcf/src/main/java/genepi/nf/test/vcf/VcfFileUtil.java

Line 14 in a0ff5c9

public static VcfFile load(Path vcfFilename) throws IOException {