Open Drdreammaerd opened 2 years ago
Hi, this looks like a problem with your pedigree file. Can you share that here or send off-line?
Hi Brent,
The attached file is the ped file and group file. For calling denovo and compside, I used group file.
Command for denovo and compside
slivar expr --vcf $vcf --alias $group --gnotate $gnomad --js $jsycw
--out-vcf $out \
--info "variant.call_rate > 0.9" \
--group-expr "denovo:denovo(kid, mom, dad) && INFO.ExAC_ALL < 0.0004" \
--group-expr "comphet_side:comphet_side(kid, mom, dad) && (
INFO.ExAC_ALL < 0.001 || INFO.x3b1000g2015aug_all < 0.001 ||
INFO.esp6500siv2_all < 0.001) "
Command for comphet
slivar compound-hets -v $vcf \
--sample-field comphet_side --sample-field denovo -p $ped > $out
Thanks,
David ---------------------------------------------PED--------------------------------------------------- AUS005 AUS005P AUS005F AUS005M 2 2 AUS007 AUS007P AUS007F AUS007M 2 2 AUS008 AUS008P AUS008F AUS008M 1 2 AUS009 AUS009P AUS009F AUS009M 1 2 AUS012 AUS012P AUS012F AUS012M 2 2 AUS017 AUS017P AUS017F AUS017M 1 2 AUS019 AUS019P AUS019F AUS019M 1 2 ------------------------------------------group-----------------------------------------------------
ok. that's too much for me to guess. I've added more info to the error message. can you try again with this attached binary (just gunzip and chmod+x) so we can narrow it down.
I'm curious why you chose to use group-expr rather than family-expr?
You can ask other questions here slivar.gz
I am just wondering where should I put the file since I am using slivar in docker.
The reason I am using group-expr, just because I thought the group file is more easy to generate for a large size cohort. Can I also use group file for family-expr? Also, if there is singleton, dual, quad. How should I indicate them in group and ped that is able to recognize by family-expr?
Thanks,
David
if your pedigree file is properly speicified, then slivar will automatically detect familys and the --family-expr stuff shown in the wiki will work for families of all sizes, including duos, multi-generational pedigrees, and so on.
I am just wondering where should I put the file since I am using slivar in docker.
which file? just mount the directory containing whichever file you need.
I am sorry if my question is not clear. Kind of new to the area. Will do my best to clarify my question. What I mean is the binary file called "slivar.gz" you attached. Do you mind to give me more detailed instruction how to use it? I am using the docker through institution cluster
Thanks,
David
oh. I see. so unzip the file and chmod +x it. Then if you put in in your working directory you can do, for example:
docker run -v$(pwd):/load ... /load/slivar expr ...
Cool, Thanks. I have chomd +x it
-rwxr-xr-x@ 1 dreammaerd staff 17M Dec 20 09:22 slivar_brent
How do I execute it?
command not found: slivar_brent
./slivar_brent
or use the linked path as shown in the example above.
Thanks brent. My colleague helps to find the problem and it works well now. The problem is in original pedigree file I didn't provide the information of parents. Somehow it works when I provide those.
Original PED
AUS005 AUS005P AUS005F AUS005M 2 2
AUS007 AUS007P AUS007F AUS007M 2 2
AUS008 AUS008P AUS008F AUS008M 1 2
AUS009 AUS009P AUS009F AUS009M 1 2
AUS012 AUS012P AUS012F AUS012M 2 2
New PED
AUS005 AUS005P AUS005F AUS005M 2 2
AUS005 AUS005F 0 0 1 1
AUS005 AUS005M 0 0 2 1
AUS007 AUS007P AUS007F AUS007M 2 2
AUS007 AUS007F 0 0 1 1
AUS007 AUS007M 0 0 2 1
AUS008 AUS008P AUS008F AUS008M 1 2
AUS008 AUS008F 0 0 1 1
AUS008 AUS008M 0 0 2 1
AUS009 AUS009P AUS009F AUS009M 1 2
AUS009 AUS009F 0 0 1 1
AUS009 AUS009M 0 0 2 1
AUS012 AUS012P AUS012F AUS012M 2 2
AUS012 AUS012F 0 0 1 1
AUS012 AUS012M 0 0 2 1
P.s. Slivar is really a wonderful tool!!!
Thanks for your kind response and help,
David
I have another question for Comp-het function, can I ask here or should I request a new thread?
here is fine, we can move to a new thread if needed. glad to hear that slivar is useful for you! I think it makes sense how you solved. The mix of groups/aliases and ped sort of hid the error that usually would be prevented by using --family-expr.
Cool thanks.
My question is what field of vep annotation it will be counted for slivar-compound-hets function? I know in the description, it said group by gene. But somehow when I use vep annotation only choose field gene, the slivar cannot run that vep annotated file by just exiting out without error message.
VEP command
/opt/vep/src/ensembl-vep/vep -i $vcf -o $out --cache --dir $cache --force_overwrite --vcf --fields "Gene"
can you show what VEP adds to the header of $out
for that?
and can you show a full CSQ field from the INFO for one variant?
Sure. The header for VEP is CSQ: Chr and position
chr1_902926_T_C T
Only Gene field
CSQ=ENSG00000272438|
All field
CSQ=C|upstream_gene_variant|MODIFIER|
|ENSG00000272438|Transcript|ENST00000607769|lncRNA|||||||||||1908|1|||
I mean can you show the actual VCF header line?
The meta-information line for VEP
##VEP="v105" time="2021-12-18 23:21:53" cache="./.vep/homo_sapiens/105_GRCh38" db="homo_sapiens_core_105_38@ensembldb.ensembl.org" ensembl-variation=105.ac8178e ensembl=105.f357e33 ensembl-funcgen=105.660df8f ensembl-io=105.2a0a40c 1000genomes="phase3" COSMIC="92" ClinVar="202106" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 39" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Gene|IMAPCT">
And it adds to "INFO" column in vcf.
This can't work:
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format:Gene|IMAPCT">
"IMAPCT" will not be understood and it needs standard VEP annotations in the output. These should be something like:
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE">
Thanks. Can you share your VEP command please?
Hi @brentp,
I ran the comphet function after calling the denovo and comp-side, and it gave me fatal error that I don't know how to fix. I have ran the same command line for another vcf, which worked pretty well.
slivar compound-hets -v $vcf --sample-field comphet_side --sample-field denovo -p $ped > $out
Error
fatal.nim(49) sysFatal Error: unhandled exception: comphet.nim(46, 12)
kid.dad != nil and kid.mom != nil and kid.dad.i != -1 and kid.mom.i != -1[AssertionDefect]
Thank you for your time and any suggestion is aprreciated,
David