The second BND locus in VCF

[Damian Loska]

Hey,

The output VCF entry looks like:

3       32112229        BND00002209     A       A]2:230735780]  300     PASS    PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv1.2.6;END=32112230;CHR2=2;POS2=230735780;

why there is no the second entry like:
2      230735780     BND00002209    C      C[3: 32112229[

It is actually important to put reciprocal BND entries in VCF, so the VEP can annotate both  breaking points. 
Is there an option to separte such entries? 

[Tobias Rausch]

Hi,

There is a script in the delly code repository that converts delly's BND calls to the breakend notation.

https://github.com/dellytools/delly/tree/main/scripts

I hope this works and please let me know if you notice any errors.

Best, Tobias

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[Damian Loska]

Thank you for the quick answer, but it doesn't work:(

python /progs/delly/scripts/delly2bnd.py -v delly.vcf -r $ref38 -o delly_bnd.vcf


Fetching breakpoint nucleotides... 20
Fetching breakpoint nucleotides... 21
Fetching breakpoint nucleotides... 22
Fetching breakpoint nucleotides... X
Fetching breakpoint nucleotides... Y
Fetching breakpoint nucleotides... KI270442.1
Fetching breakpoint nucleotides... KI270438.1
Processing... 1
Processing... 2
Traceback (most recent call last):
  File "/mnt/data/NGS/progs/delly/scripts/delly2bnd.py", line 105, in <module>
    record.CHROM = chrom2
AttributeError: attribute 'CHROM' of 'cyvcf2.cyvcf2.Variant' objects is not writable


Best, Damian

[Tobias Rausch]

Looks like you are using an outdated cyvcf2 version. What version of cyvcf2 are you using?

To view this discussion on the web visit https://groups.google.com/d/msgid/delly-users/43d68c46-ecb7-4c74-a515-fb005ad15516n%40googlegroups.com.

[Damian Loska]

Indeed. Now it works after:
pip install --upgrade cyvcf2

Thanks!

[Damian Loska]

one note: it works, but it copies INFO and FORMAT tags. I believe, every locus/position shoud have it's own tags and metrices (read depths, qualities etc).

Best regards
DL

[Damian Loska]

also such issue appears:
bcftools annotate -x ^INFO/END,INFO/SVLEN,INFO/SVTYPE,INFO/IMPRECISE -O v delly.vcf

SVTYPE=DEL[W::vcf_parse_info] INFO 'MATEID' is not defined in the header, assuming Type=String
Encountered an error, cannot proceed. Please check the error output above.
If feeling adventurous, use the --force option. (At your own risk!)

[Tobias Rausch]

The script adds MATEID to the header: https://github.com/dellytools/delly/blob/c5ac173d6801f57a0563d4ddee216bcddd5bab2d/scripts/delly2bnd.py#L58

To view this discussion on the web visit https://groups.google.com/d/msgid/delly-users/a3559c02-aef2-425f-8c5a-dd152030945bn%40googlegroups.com.

[Damian Loska]

Right, my bad, I took the header from a file before