-
I have a gVCF where the allele order of alleles not present in the genotype (`FORMAT/GT`) change when I run GATK multiple times. The resultant allele-specific values (eg. `FORMAT/PL`) all match after…
-
When I use gatk to CombineGVCFs, the following error occurs: "Cannot read file because no suitable codecs found".
How can I solve this problem?
-
This subworkflow will cover the gatk4 best practices workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- starting with the analys…
-
Hey guys,
Probably a stupid question but is there a way (or a simple to add feature?) to choose the name of the genotype fields when creating a merged pVCF? For example, I am trying to create a pV…
-
I have a fairly mundane need for pi and fst estimates that are in the ballpark but not necessarily the most accurate possible. We have a huge number of samples that I don't have the time or resources …
-
Is there a document or good summary of the different types / conventions for VCF? For example, VCF, sites-only VCF, gVCF, pVCF, spVCF. EG:
- A gVCF (Genomic VCF) contains information for every posi…
-
WhatsHap 2.1
Python 3.11.6
pip 23.3.2
Ubuntu 20.04.1
I'm trying to phase a human gVCF. It has 5740675 rows and it has 4 grandparents, 2 parents and 5 children. The phasing needs to be done by 11…
-
Hi,
To report the presence of both haploid and diploid genotypes in the output from GVCF Genotyper Version: 2.1.0. The file is merged.vcf.gz dowloaded from BaseSpace.
Since these are human dat…
-
User is seeing non-ref blocks with GQ=0 even though bamout shows reads covering that region. Example: chr1 14155446 . C . . END=14155446 GT:DP:GQ:MIN_DP:PL 0/0: 100:0: 100 :0,0,0
Discussed this at…
-
Improve VCF2Genome to be able to read a normal VCF file (not EMIT_ALL_SITES, rather EMIT_CONFIDENT_SITES or
EMIT_DEFAULT)