What does the position column in the VCF file from PostprocessGermlineCNVCalls refer to?

Question

[Frieda]

Hello,

PostprocessGermlineCNVCalls post-processes the output of GermlineCNVCaller and generates VCFs with deletions and duplications.

According to samtools documentation (https://samtools.github.io/hts-specs/VCFv4.3.pdf), if any of the ALT alleles in a VCF is a symbolic allele (<DUP> or <DEL>), then POS denotes the coordinate of the base preceding the polymorphism.

Does the POS column in the output VCF file created by PostprocessGermlineCNVCalls refer to the first position of the duplication/deletion event or the preceding base?

[Pierre Lindenbaum]

Does the POS column in the output VCF file created by PostprocessGermlineCNVCalls refer to the first position of the duplication/deletion event or the preceding base?

does it really matter ? PostprocessGermlineCNVCalls is part of the gakCNV workflow https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants ) which starts with an "arbitrary" bin number in PreprocessIntervals (--bin-length 1000)

[Frieda]

@Pierre Lindenbaum In the genotyped-segments output vcf, each segment from the intervals-list file is annotated as a CNV. So I guess for the genotyped-segments file, the bin size does not matter.

example:

intervals-list file:

NC_000001.11 65315 65823 + .

genotyped-segment vcf:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1
NC_000001.11    65315   CNV_NC_000001.11_65315_65823    N   <DEL>   176.97  .   END=65823   GT:CN:NP:QA:QS:QSE:QSS  1/1:0:1:177:177:177:177