Menu
▾
▴
[Gmod-ajax] Error: Cannot read property slice of null for VCF + CSI
|
From: Hans Vasquez-G. <hav...@uc...> - 2019-06-05 22:30:10
|
Hi all, I am trying to load a new VCF+CSI file to my jbrowse. However, I am getting the following error: Cannot read property slice of null [image: Screen Shot 2019-06-05 at 2.56.38 PM.png] You can view at this link here <https://dubcovskylab.ucdavis.edu/ecotilling/?loc=chr1A%3A189961459..189962859&tracks=DNA%2CHighConfGenes%2Ccombinedmaps2019&addFeatures=%5B%7B%22seq_id%22%3A%22chr7A%22%2C%20%22start%22%3A%20674082831%2C%20%22end%22%3A%20674082918%2C%20%22name%22%3A%20%22MyBLASTHit_1%22%2C%20%22description%22%20%3A%20%22evalue%205.74e-37%22%7D%5D&addTracks=%5B%7B%22label%22%3A%22blast%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%2C%20%22key%22%3A%22BlastHSP%20Results%22%7D%5D%0A&highlight=>. And here is a small sample of the VCF. It seems like maybe the CSI is invalid? However, it looks like there is data in the file. Any advice would be greatly appreciated. ##fileformat=VCFv4.0 ##fileDate=201964 ##source=Kronos ##referece=IWGSC ##phasing=full ##CHROM POS ID REF ALT QUAL FILTER INFO ##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" ##SnpEffCmd="SnpEff iwgsc1 ./combined_maps.vcf " ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> chr1A 1145762 Kronos2392:G1145762A G A 40.0 Pass seed_avail=Kronos2392;hethom=hom;ANN=A|downstream_gene_variant|MODIFIER|TraesCS1A01G001800|TraesCS1A01G001800|transcript|TraesCS1A01G001800.1|protein_coding||c.*164G>A|||||164|,A|intergenic_region|MODIFIER|TraesCS1A01G001800-TraesCS1A01G001900|TraesCS1A01G001800-TraesCS1A01G001900|intergenic_region|TraesCS1A01G001800-TraesCS1A01G001900|||n.1145762G>A|||||| chr1A 1159612 Kronos473:G1159612A G A 40.0 Pass seed_avail=Kronos473;hethom=het;ANN=A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.10|protein_coding|9/9|c.1436C>T|p.Ser479Phe|1436/1527|1436/1527|479/508||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.1|protein_coding|10/10|c.1331C>T|p.Ser444Phe|1331/1422|1331/1422|444/473||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.2|protein_coding|10/10|c.1328C>T|p.Ser443Phe|1328/1419|1328/1419|443/472||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.3|protein_coding|9/9|c.1430C>T|p.Ser477Phe|1430/1521|1430/1521|477/506||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.4|protein_coding|10/10|c.1331C>T|p.Ser444Phe|1331/1422|1331/1422|444/473||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.5|protein_coding|9/9|c.1157C>T|p.Ser386Phe|1157/1248|1157/1248|386/415||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.6|protein_coding|10/10|c.1340C>T|p.Ser447Phe|1340/1431|1340/1431|447/476||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.7|protein_coding|10/10|c.1337C>T|p.Ser446Phe|1337/1428|1337/1428|446/475||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.8|protein_coding|10/10|c.1340C>T|p.Ser447Phe|1340/1431|1340/1431|447/476||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.9|protein_coding|10/10|c.1343C>T|p.Ser448Phe|1343/1434|1343/1434|448/477||,A|downstream_gene_variant|MODIFIER|TraesCS1A01G002000|TraesCS1A01G002000|transcript|TraesCS1A01G002000.1|protein_coding||c.*4356C>T|||||4356| chr1A 1159898 Kronos2566:C1159898T C T 40.0 Pass seed_avail=Kronos2566;hethom=het;ANN=T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.10|protein_coding|9/9|c.1150G>A|p.Asp384Asn|1150/1527|1150/1527|384/508||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.1|protein_coding|10/10|c.1045G>A|p.Asp349Asn|1045/1422|1045/1422|349/473||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.2|protein_coding|10/10|c.1042G>A|p.Asp348Asn|1042/1419|1042/1419|348/472||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.3|protein_coding|9/9|c.1144G>A|p.Asp382Asn|1144/1521|1144/1521|382/506||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.4|protein_coding|10/10|c.1045G>A|p.Asp349Asn|1045/1422|1045/1422|349/473||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.5|protein_coding|9/9|c.871G>A|p.Asp291Asn|871/1248|871/1248|291/415||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.6|protein_coding|10/10|c.1054G>A|p.Asp352Asn|1054/1431|1054/1431|352/476||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.7|protein_coding|10/10|c.1051G>A|p.Asp351Asn|1051/1428|1051/1428|351/475||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.8|protein_coding|10/10|c.1054G>A|p.Asp352Asn|1054/1431|1054/1431|352/476||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.9|protein_coding|10/10|c.1057G>A|p.Asp353Asn|1057/1434|1057/1434|353/477||,T|downstream_gene_variant|MODIFIER|TraesCS1A01G002000|TraesCS1A01G002000|transcript|TraesCS1A01G002000.1|protein_coding||c.*4070G>A|||||4070| Cheers, -Hans |
