Inquiry about slivar software applicability

[jinhua2024]

Dear Author's,

I am currently researching trio family genetic diseases in pigs. I am very interested in the slivar software you developed and would like to inquire whether it is suitable for analyzing pig VCF data, particularly for identifying genetic variants associated with diseases. If it is applicable, could you kindly provide some tutorials or suggestions for using it with pig data?

Thank you for your help, and I look forward to your response.

Best regards,
jinhua

[brentp]

Hi Jinhua, slivar is agnostic to the organism. If you have a pedigree file for your pigs, then you can use it as explained in the documentation (which does use humans as an example).
If you have a specific question, along with a pedigree file, I can probably help you more.

[jinhua2024]

Dear Professor Brentp,
I hope this email finds you well. I have been utilizing your exceptional tool, slivar, for variant filtering in my research. I am truly grateful for the development of such a powerful software.
Currently, I am conducting research on rare genetic diseases in pigs and aim to employ the compound heterozygous model for analysis. I have already made some attempts in this regard. Given that my pedigree contains multiple affected individuals (please find the pedigree file in the attachment), I wish to identify and output the compound heterozygous variants common to all affected individuals. Could you please offer some guidance and suggestions to help me optimize my analysis workflow?
Thank you very much for your time and for creating such a valuable tool. I look forward to your reply.
Best regards,
jinhua

y72207_family.ped.txt

[brentp]

Hi, so you can use slivar expr first like this:

slivar expr \
   --ped $your.ped \
    --trio 'comphet_side:comphet_side(kid, mom, dad)' \
    ...

and then run:

slivar compound-hets -v vcfs/$cohort.vcf \
    --sample-field comphet_side 

if you try that and let me know any issues, I can help further.

[jinhua2024]

y72207_chhet_all_1000lines.vcf.txt

Hello Brent,

I am working with slivar to detect compound heterozygous variants in my family data.
My PED file looks like this:

AAA Y72207_326 . . 1 1
AAA 4274_334 . . 2 1
AAA 6497_309 . . 2 1
AAA 4255_234 . . 2 1
AAA D2_317 Y72207_326 4274_334 2 2
AAA D3_323 Y72207_326 4255_234 2 2
AAA D4_318 Y72207_326 4274_334 2 2
AAA D5_316 Y72207_326 4274_334 2 2
AAA D6_314 Y72207_326 4274_334 2 2
AAA M2_324 Y72207_326 4274_334 2 2
AAA FM4_488 Y72207_326 4274_334 2 1
AAA FM5_319 Y72207_326 4274_334 2 1
AAA FM6_325 Y72207_326 4274_334 2 1
AAA FM2_313 Y72207_326 4274_334 2 1
I first ran:

slivar expr
--vcf /Y72207_family/32_snp_indel_pass_y72207.ann.vcf.gz
--ped y72207_family.ped
--trio 'comphet_side:comphet_side(kid, mom, dad)'
--js slivar-functions.js
-o 32_snp_indel_pass_y72207.expr.vcf.gz

Then I ran:

slivar compound-hets
-v 32_snp_indel_pass_y72207.expr.vcf.gz
-p y72207_family.ped
--sample-field comphet_side
-o y72207_chhet_all.vcf

Now I would like to further filter the results to keep only compound heterozygous variants that are present in all affected individuals in my pedigree.

Could you please advise:

Is there a recommended slivar expression or workflow to filter the compound-hets output so that only variants present in all affected individuals remain?

Should this filtering be done directly in slivar (e.g., using slivar expr with genotype conditions) or after compound-hets with a custom script?

Thank you very much for your time and for developing slivar!

Best regards,
Jinhua