Representation of GT:DS INFO tag for a missing marker in a VCF file
What would be the best way of representing the GT:DS INFO tag for a missing (unimputed)marker in a VCF file? Is ./.:. correct?
vcf
bcftools
• 683 views
•
link
written
by
Mwangana •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?
written by Nadia •Hello, I have a VCF file with GT:HDS (haploid dosage) values, but I need to generate GT:DS (diploid dosage), since this is the most common …
-
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
written by Марта •Hello, all. I'm trying to add FORMAT/TAG annotation to all samples in my vcf file and I want it to be a missing value (".") …
-
Commands to do the following in BCFtools or recommendations for another tool
written by ex_nihilo •I am looking for a VCF manipulation tool (or tools) that will allow me to do the following: - Add arbitrary INFO/FORMAT tags to a …
-
Partition reads in BAM file by MAG
written by Gio •Hi all, I have bins representing MAGs. I am now interested in partitioning the reads in my BAM files by MAG. The way I believe …
-
convert beagle genotypes to vcf
written by bsp017 •Hi, I have a phased beagle file which I generated through Angsd v0.935. I would like to use the beagle utility program beagle2vcf.jar. However I …
-
Dealing with half missing calls in ".ped" file
written by reza.jabalI am trying to convert my VCF files to plink format for some downstream processing in PLINK. Since VCF half calls are coded as `"0/.", …
-
bcftools annotate picks one attribute but not another
written by RamHello, I've run into a weird error and would like to figure out what's going on. I'm annotating a VCF file from a library VCF …
-
Convert imputed genotypes from IMPUTE2 dosage .gen/.info to vcf format
written by 1888Hi, Is there an easy way to convert imputed genotypes from probability format like this: --- rs190467660 10010504 A C 0.929 0.070 0 0.895 0.102 …
-
No vcf output from vcftools
written by axelwilhelmI thought this command would give me a new vcf file without the individuals in the text file: vcftools --gzvcf mergedPF.vcf.gz --remove listPnsToRemoveFromMergedVcf.txt --out filtMergedPTrios …
-
Filtering Vcf Files
written by rickyflintoff •<p>I am trying to subset a VCF file by a tag in INFO column. The tag is a triplet and I want to threshold by …