Overlaps with another variant

[karel-brinda]

Why are variants overlapping (it should not happen)?

29 of 47 steps (62%) done
rule 54:
abix, 2_alignments.itref/1_reference/00002.fa, 2_alignments.itref/1_reference/00002.fa.fai, 2_alignments.itref/5_vcf/00002.vcf.gz  

The site gi|386853410|ref|NC_017717.1|:27511 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:27512 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:56819 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:79988 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:122891 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:208363 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:225832 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:256017 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:286078 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:293988 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:307690 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:325324 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:421297 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:505903 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:548364 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:548367 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:676833 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:710469 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:755389 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:873401 overlaps with another variant, skipping...
The site gi|386853410|ref|NC_017717.1|:888498 overlaps with another variant, skipping...

[jimguo]

saw the same problem.

[karel-brinda]

@jimguo Hello, thank you for your message. I was dealing with this issue but I eventually decided not to do any particular fix for it. Now I don't remember why I decided so -- probably because these non-updated SNPs get updated in the next iteration and the impact on final statistics is almost zero... Maybe I will look at it once again.

In which exact experiment/run did you observe it?