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 https://github.com/brentp/slivar/issues/166#issuecomment-1969690444, 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 https://github.com/brentp/slivar/issues/166#issuecomment-1975129505, 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.