error message

[monaallouba]

Hello,

I tried using slivar on a single trio but I got this error which I do not understand

[slivar] 3 samples matched in VCF and PED to be evaluated
[slivar] message for /mnt/my_work/Mona/unexplained_HCM_WES/43268/slivar_script/gnomad.hg38.genomes.v3.fix.zip:

created on:2019-11-15
[slivar tsv] warning! didn't find ANN in header in /mnt/my_work/Mona/unexplained_HCM_WES/43268/results/FINAL_43268_de_novo_annotated_VEP_all_variants.vcf.gz trying other fields
[slivar tsv] warning! didn't find BCSQ in header in /mnt/my_work/Mona/unexplained_HCM_WES/43268/results/FINAL_43268_de_novo_annotated_VEP_all_variants.vcf.gz trying other fields
[slivar] evaluating on 1 trios
fatal.nim(53) sysFatal

Error: unhandled exception: gnotate.nim(121, 12) g.zip.readInto(&"sli.var/{chrom}/gnotate-{field_name}.bin", g.values[field_i]) [AssertionDefect]

Could you please help me address this error
Many thanks

[brentp]

Hi, I am guessing that your zip file is corrupt, or not fully downloaded.

[monaallouba]

Thank you very much for your prompt response. I used wget https://slivar.s3.amazonaws.com/gnomad.hg38.genomes.v3.fix.zip and it showed that the download 100% complete. Could it be a different issue?

[monaallouba]

I downloaded it again and it worked. Thank you very much!

[monaallouba]

Hello, I ran the slivar script on a WES trio and got the output attached Could you please let me know how i can identify the 12 de novo variants and 93 recessive variants in the output VCF (in which column are they) Many thanks All the best, Mona

…

On Wed, Feb 28, 2024 at 9:24 PM Brent Pedersen ***@***.***> wrote: Hi, I am guessing that your zip file is corrupt, or not fully downloaded. — Reply to this email directly, view it on GitHub <#166 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A73WRQSQZFMUFEWJXA4HB6LYV576FAVCNFSM6AAAAABD6SUYZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRZGY4TANBUGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[brentp]

Hi Mona, what command did you run?

[monaallouba]

Hi Brent, Thank you for your prompt response. I applied this command: ./slivar expr --vcf $vcf --ped $ped -o /mnt/my_work/Mona/unexplained_HCM_WES/43268/slivar_script/43268_trio_slivar.vcf --pass-only -g /mnt/my_work/Mona/unexplained_HCM_WES/43268/slivar_script/gnomad.hg38.genomes.v3.fix.zip.1 --info 'INFO.impactful && INFO.gnomad_popmax_af < 0.01 && variant.FILTER == "PASS" && variant.ALT[0] != "*"' --js slivar-functions.js --family-expr 'recessive:fam.every(segregating_recessive)' --family-expr 'x_denovo:(variant.CHROM == "X" || variant.CHROM == "chrX") && fam.every(segregating_denovo_x) && INFO.gnomad_popmax_af < 0.001' --trio 'comphet_side:comphet_side(kid, mom, dad) && INFO.gnomad_nhomalt < 10' Thank you very much All the best, Mona

…

On Sun, Mar 3, 2024 at 1:31 PM Brent Pedersen ***@***.***> wrote: Hi Mona, what command did you run? — Reply to this email directly, view it on GitHub <#166 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A73WRQUQ467Q2FESCI7RNNDYWMCYNAVCNFSM6AAAAABD6SUYZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZVGEZDSNJQGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[brentp]

so you have:

--family-expr 'recessive:fam.every(segregating_recessive)' 
--family-expr
'x_denovo:(variant.CHROM == "X" || variant.CHROM == "chrX") &&
fam.every(segregating_denovo_x) && INFO.gnomad_popmax_af < 0.001' 
--trio 'comphet_side:comphet_side(kid, mom, dad) && INFO.gnomad_nhomalt < 10'

so you can look in the INFO field of the output vcf and find variants with recessive= in the INFO; what follows the = will be the list of samples that met that filter. Likewise for x_denovo and comphet_side.