sent empty file-name to xopen.Ropen or no records found with 'gene' type in gff

[asmlgkj]

Dear professor, Thanks a lot for such a good comprehensive tool. can you help to me to look at this question? with or without gff both does not work; I have done successfully with call command

[brentp]

Hi, you need to send the gff, and the gff must have records of type 'gene'. If you can share the gff, then I could see what the problem is...

I would recommend to use svpack for structural variant annotation. I think it does a good job.

[asmlgkj]

gff downloaded from gencode v37;gencode.v38lift37.annotation.gff3; or can you tell me which gff is ok for hg19 thanks a lot

[brentp]

hi, smoove is expecting the final column to indicate Name=$name, but your gff uses gene_name=$name. You can use sed or perl or python to change gene_name= to Name= and then smoove will be able to get the information it needs.

[asmlgkj]

thanks a lot; where do you downloaded the gff for using; after I downloadef gff from http://ftp.ensembl.org/pub/grch37/current/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.chr.gff3.gz ; it works now. in the vcf header, has a line like this; ##INFO=<ID=smoove_gene,Number=.,Type=String,Description="genes overlapping variants. format is gene|feature:nfeatures:nbases,...">;

##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">

I have a variant annotation like following:

chr7 55103208 450 N <DEL> 277.84 . SVTYPE=DEL;SVLEN=-186;END=55103394;STRANDS=+-:50;IMPRECISE;CIPOS=-30,34;CIEND=0,1;CIPOS95=-4,4;CIEND95=0,0;SU=50;PE=50;SR=0;AC=1;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:200:277.84:-348,-321,-1550:2056:1839:216:1838:215:937:0:191:901:24:0.1

does it mean: the ref has 1838 reads. alt has 215 reads; and the freq is 215/(215+1838)=0.1

[brentp]

QA and QR are quality. For ref and alt counts, use RO, AO

[vitty0513]

Dear, I met the same problem and my gff is: LG1 EVM gene 8435 27996 . - . ID=Ofur01G000010 LG1 EVM mRNA 8435 27996 . - . ID=Ofur01G000010.1;Parent=Ofur01G000010 LG1 EVM CDS 8435 8524 . - 0 ID=CDS:Ofur01G000010.1:8435;Parent=Ofur01G000010.1; LG1 EVM exon 8435 8524 . - . ID=exon:Ofur01G000010.1:8435;Parent=Ofur01G000010.1; LG1 EVM CDS 12826 12861 . - 0 ID=CDS:Ofur01G000010.1:12826;Parent=Ofur01G000010.1; LG1 EVM exon 12826 12861 . - . ID=exon:Ofur01G000010.1:12826;Parent=Ofur01G000010.1; LG1 EVM CDS 15079 15154 . - 1 ID=CDS:Ofur01G000010.1:15079;Parent=Ofur01G000010.1; LG1 EVM exon 15079 15154 . - . ID=exon:Ofur01G000010.1:15079;Parent=Ofur01G000010.1; LG1 EVM CDS 16900 16974 . - 1 ID=CDS:Ofur01G000010.1:16900;Parent=Ofur01G000010.1; LG1 EVM exon 16900 16974 . - . ID=exon:Ofur01G000010.1:16900;Parent=Ofur01G000010.1; LG1 EVM CDS 27003 27175 . - 0 ID=CDS:Ofur01G000010.1:27003;Parent=Ofur01G000010.1; LG1 EVM exon 27003 27175 . - . ID=exon:Ofur01G000010.1:27003;Parent=Ofur01G000010.1; LG1 EVM CDS 27448 27597 . - 0 ID=CDS:Ofur01G000010.1:27448;Parent=Ofur01G000010.1; LG1 EVM exon 27448 27597 . - . ID=exon:Ofur01G000010.1:27448;Parent=Ofur01G000010.1; LG1 EVM CDS 27633 27692 . - 0 ID=CDS:Ofur01G000010.1:27633;Parent=Ofur01G000010.1; LG1 EVM exon 27633 27692 . - . ID=exon:Ofur01G000010.1:27633;Parent=Ofur01G000010.1; LG1 EVM CDS 27778 27996 . - 0 ID=CDS:Ofur01G000010.1:27778;Parent=Ofur01G000010.1; LG1 EVM exon 27778 27996 . - . ID=exon:Ofur01G000010.1:27778;Parent=Ofur01G000010.1;

Could you please see what the problem is? Many thanks

[brentp]

@vitty0513 can you report the exact error you are seeing? smoove expects there to be a Name= field in the gff, it doesn't look like yours has this.

[vitty0513]

This is my log: [smoove] 2023/06/12 15:56:54 starting with version 0.2.8 2023/06/12 15:56:56 no records found with 'gene' type in gff

[brentp]

The error message isn't very helpful, but you'll need a gff with a Name attribute for smoove to work.