Insert SVs in vcfs

[jackieduckie]

I would like to generate reads with specified SVs inserted. It doesn't look like it's supported. The vcfs are skipped due to non-ACGT character in the ALT field.

---

reading input VCF...
Warning: Found variants without a GT field, assuming heterozygous...
found 6 valid variants in input vcf.

• 0 variants skipped: (qual filtered / ref genotypes / invalid syntax)
• 0 variants skipped due to multiple variants found per position

---

found 0 valid variants for chr1 in input VCF...
6 variants skipped...

• [0] ref allele does not match reference
• [0] attempting to insert into N-region
• [6] alt allele contains non-ACGT characters

---

My variants are something like this:

chr1 30001110 bnd_5 G G[chrM:2100[ . . .
chr1 30001111 bnd_6 G ]chrM:2200]G . . .

Thanks
JD

[zstephens]

Greetings! Unfortunately the simulator can only accept deletions or insertions (or combinations of them, e.g. inversions) and does not yet support translocations or other interchromosomal SVs. It has been on my feature wishlist for awhile but would be a bit of an undertaking to implement given how some parts of the simulation are currently implemented.

[yangyxt]

Greetings! Unfortunately the simulator can only accept deletions or insertions (or combinations of them, e.g. inversions) and does not yet support translocations or other interchromosomal SVs. It has been on my feature wishlist for awhile but would be a bit of an undertaking to implement given how some parts of the simulation are currently implemented.

Isn't any SV can be represented by ins or del or the combination of them? ?