What is "*" in the ALT field of my VCF file

I get the following line in my vcf file generated with GATK:

YALI0A  9035  .    C   A,*   67408.50  PASS  AC=11,2;AF=0.196,0.036;AN=56 GT:AD:DP:GQ:PL 2:0,0,233:233:99:9791,9791,0  1:30,70,0:100:99:2565,0,2715

Does anyone know what the "*" means in the ALT field?

vcf gatk

• 2,437 views • link

updated 5.8 years ago by Pierre Lindenbaum

• written 5.8 years ago by Frédéric Bigey

1 answer

https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-

We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest.

• 0 views • link

written 5.8 years ago by Pierre Lindenbaum

More posts like this

Merging VCFs from same sample created by different variant callers and adding new INFO field for va…
written 4.4 years ago by Jordi •

Hi, I am generating 2 distinct SNVs/small indels for each sample from WGS data. The two VCFs are generated by `gatk HaplotypeCaller` and `deepvariant`. After …
PGT only available for some variants in GATK .vcf
written 4.7 years ago by michael.flower.14 •

I've got a vcf file someone else prepared using GATK. I'm interested in the phasing information in the PGT tag e.g. 0|1. This information seems …
print only columns with data from every line
written 5.0 years ago by HL •

Hi, I have a vcf file where is about 60 000 columns. Here is example of the first three lines: #CHROM POS ID REF ALT …
merging vcf files with sample information
written 6.5 years ago by tothepoint

I am working on gwas data and ran bwa, GATK pipeline and generated vcf file of all the samples. After merging the vcf file using …
VariantsToTable not properly handle AD greater than 100
written 7.0 years ago by functional.genomics •

I am trying to extract info from a vcf file using the following command and encountered a problem: gatk VariantsToTable -R $REF -V final_SNP.vcf -F …
one variant's AD tag in VCF file shows 0,0
written 9.2 years ago by sxzhuxu •

I find a variant in my vcf file. This variant's DPis 232, however the AD is '0,0'. I can't understand why REF and ALT allele …
Minor Allele Frequency calculation from VCF file
written 10.9 years ago by a.james

Hello All I am using [GATK RNA-seq variant pipeline][1] for finding mutation/variant calling on the list of gene given in the following command line java-1.7 …
Vcf-Consensus To Generate Consensus File
written 14.0 years ago by Nupur G •

I have a VCF file and a reference fasta file, and am trying to create a consensus sequence using vcf-consensus. First I create a tabix …
Missing Allele Balance Tag In Vcf File
written 14.3 years ago by Johan

I have a problem with my vcf files. I have called SNPs using the GATK UnifiedGenotyper with the AlleleBalance annotator. For some of the SNPs …
Unifiedgenotyper Bug?
written 14.3 years ago by Leandro Batista •

Hi everyone, I'm calling SNPs with UnifiedGenotyper: java -Xmx2g -jar /Volumes/DroboLeandro/Analysis/Software/GenomeAnalysisTK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /Volumes/DroboLeandro/Analysis/Genomes/Reference/NCBIM37.chr.fa -I BALBcByJ.recal.bam --dbsnp /Volumes/DroboLeandro/Analysis/dbSNP/dbSNP.vcf --genotype_likelihoods_model SNP --metrics_file BALBcByJ.metrics.snp.txt -stand_call_conf 30 …