Comments (11)
tobiasrausch
commented on September 27, 2024
1
Ensembl and UCSC use different feature values. By default, sansa uses "gene" as the feature value (fine for Ensembl) but for UCSC you need to specify "transcript".
sansa annotate -f transcript -g hg38.knownGene.gtf.gz ADB_LL.delly.SV.vcf.gz
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leehs96
commented on September 27, 2024
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT JSH_LN_Lt ADB_Blood LMS_Blood SJH_Blood JSH_Blood 10847652_NT 12140782_Blood
chr1 63400385 DEL00000000 A <DEL> 0 LowQual IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr1;END=209990649;PE=2;MAPQ=37;CT=3to5;CIPOS=-519,519;CIEND=-519,519;RDRATIO=1.0334;SOMATIC GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-4.58867,0,-44.725:46:PASS:0:18476967:0:-1:8:3:0:0 0/0:0,-8.1278,-162:81:PASS:0:18508703:0:-1:27:0:0:0 0/0:0,-6.02059,-120:60:PASS:0:17239644:0:-1:20:0:0:0 0/0:0,-2.40824,-48:24:PASS:0:16914471:0:-1:8:0:0:0 0/0:0,-4.81643,-93.9999:48:PASS:0:17879783:0:-1:16:0:0:0 0/0:0,-3.91338,-78:39:PASS:0:18005816:0:-1:13:0:0:0 0/0:0,-8.42883,-167.7:84:PASS:0:17091360:0:-1:28:0:0:0
chr1 246232881 DUP00000001 C <DUP> . PASS IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr1;END=246233246;PE=3;MAPQ=36;CT=5to3;CIPOS=-393,393;CIEND=-393,393;RDRATIO=1.4739;SOMATIC GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-4.88483,0,-59.5916:49:PASS:3645:12321:3421:3:12:3:0:0 0/0:0,-4.50384,-71.5884:45:PASS:4352:6450:3251:2:15:0:0:0 0/0:0,-1.16884,-9.36473:12:LowQual:1356:1997:332:2:4:0:0:0 0/0:0,-2.40646,-41.0982:24:PASS:3547:10813:2313:4:8:0:0:0 0/0:0,-2.35972,-37.8515:24:PASS:3319:10219:2997:3:8:0:0:0 0/0:0,-5.29267,-88.5741:53:PASS:5360:7338:6727:1:18:0:0:0 0/0:0,-3.57627,-56.4639:36:PASS:3338:4977:3309:1:12:0:0:0
this is how my vcf file looks like except header region
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tobiasrausch
commented on September 27, 2024
Hi,
Are you using the release version or the latest github code? I think I fixed this already in the latest code.
Thanks, Tobias
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leehs96
commented on September 27, 2024
thanks for fast reply
i installed sansa with conda and my sansa version is 0.07 which is release version.
should i delete it and reinstall with lastest github code?
**********************************************************************
Program: Sansa
This is free software, and you are welcome to redistribute it under
certain conditions (BSD License); for license details use '-l'.
This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'.
Sansa (Version: 0.0.7)
Contact: Tobias Rausch ([email protected])
**********************************************************************
Usage: sansa <command> <arguments>
Commands:
annotate annotate VCF file
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tobiasrausch
commented on September 27, 2024
Yes, that fix happened after the release of v0.0.7. I have updated now the bioconda version with a new release v0.0.8.
https://anaconda.org/bioconda/sansa
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leehs96
commented on September 27, 2024
hi @tobiasrausch
thanks for your kindness
yes, i re-download newly updated conda version (0.0.8)
and error message that i've mentioned was gone.
that's really greatful
but, i have another issue when i run sansa
my command :
sansa annotate -g hg38.knownGene.gtf.gz ADB_LL.delly.SV.vcf.gz
and error message :
[2021-Apr-06 11:40:35] sansa annotate -g hg38.knownGene.gtf.gz ADB_LL.delly.SV.vcf.gz
[2021-Apr-06 11:40:35] Parse SV annotation database
[2021-Apr-06 11:40:35] Parsed 1 out of 1 VCF/BCF records.
[2021-Apr-06 11:40:35] GTF feature parsing
Error parsing GTF/GFF3/BED file!
my GTF file was downloaded from here :
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/
and my vcf form :
.....header region
##contig=<ID=HLA-DRB1*15:01:01:02,length=11571>
##contig=<ID=HLA-DRB1*15:01:01:03,length=11056>
##contig=<ID=HLA-DRB1*15:01:01:04,length=11056>
##contig=<ID=HLA-DRB1*15:02:01,length=10313>
##contig=<ID=HLA-DRB1*15:03:01:01,length=11567>
##contig=<ID=HLA-DRB1*15:03:01:02,length=11569>
##contig=<ID=HLA-DRB1*16:02:01,length=11005>
##INFO=<ID=RDRATIO,Number=1,Type=Float,Description="Read-depth ratio of tumor vs. normal.">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic structural variant.">
##bcftools_viewVersion=1.8+htslib-1.8
##bcftools_viewCommand=view /users/hslee/cancer/WGS_hg38/SV/delly/ADB_LL.delly.SV.bcf; Date=Wed Mar 31 00:20:53 2021
#CHROM[1] POS[2] ID[3] REF[4] ALT[5] QUAL[6] FILTER[7] INFO[8]
chr5 648742 DUP00000003 G <DUP> . LowQual IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=
thanks in advance again
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leehs96
commented on September 27, 2024
oh i solved this problem with Ensembl GFF3.gz format.
i can't figure it out why general GTF format doesn't work but .. it works with GFF3.gz format anyway.
thanks @tobiasrausch
have a nice day!
i'll close this issue
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leehs96
commented on September 27, 2024
oh, you're right
it runs perfectly
thanks for your advice
and thanks for this beautiful work as well
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Sherry520
commented on September 27, 2024
Ensembl and UCSC use different feature values. By default, sansa uses "gene" as the feature value (fine for Ensembl) but for UCSC you need to specify "transcript".
sansa annotate -f transcript -g hg38.knownGene.gtf.gz ADB_LL.delly.SV.vcf.gz
I downloaded gff3.gz from here: http://ftp.ensemblgenomes.org/pub/plants/release-51/gff3/zea_mays/
And run command as flows,
sansa_v0.0.8 annotate -g Zea_mays.Zm-B73-REFERENCE-NAM-5.0.51.gtf.gz ../03-SV/P1_vs_P2.somatic.vcf
I also try '-f transcript' or with GTF file, but all get the same error as flows:
[2021-Dec-17 18:21:06] Parse SV annotation database
[2021-Dec-17 18:21:07] Parsed 13276 out of 13276 VCF/BCF records.
[2021-Dec-17 18:21:07] GTF feature parsing
Error parsing GTF/GFF3/BED file!
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tobiasrausch
commented on September 27, 2024
I think the problem is the attribute (-i). It's not called gene_name in your case but gene_id.
sansa annotate -i gene_id -f gene ...
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Sherry520
commented on September 27, 2024
Yes, -i gene_id is OK, I misunderstand the meaning of the attribute (-i).
But the results showed some SVs were annoted with multi genes, even when I used an explicit option "-s best".
id000000657 DEL00001498 1 305386125 1 305386255 DEL00001498 720 DEL 3to5 130 Zm00001eb064600(0;+),Zm00001eb064610(919;+) Zm00001eb064600(0;+),Zm00001eb064610(789;+)
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发件人: "dellytools/sansa" ***@***.***>;
发送时间: 2021年12月17日(星期五) 晚上11:23
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主题: Re: [dellytools/sansa] sansa annotate error what(): bad lexical cast: source type value could not be interpreted as target (#3)
I think the problem is the attribute (-i). It's not called gene_name in your case but gene_id.
sansa annotate -i gene_id -f gene ...
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