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The phase 1 snv annotations refer to a file without AF field. Resulting in missing AF fields.
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After https://github.com/broadinstitute/gatk/pull/792 is merged, ensure that our version of `SelectVariants` is as fast or faster than the GATK3 version on typical inputs.
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Hi I am trying to perform a validation of a set of called variants against a truth set that I have generated which is in vcf format
```
##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER IN…
kevjp updated
9 years ago
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Some things to consider:
- Make VCF meta data smaller
- Move comparison dropdown near CQL search
- Bring VCF comparison table near CQL search
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Hi,
I have below indel detected by Freebayes:
chr10 88679046 . GAGCCCTG GTGTAG
After running the normalization using vt, it became:
chr10 88679047 . AGCCCT TGTA
This i…
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```
What steps will reproduce the problem?
1. Create a VCF file a.vcf with this line:
20 1711570 . T TG 59 PASS
DP=173;NF=0;NR=0;NRS=5;NFS=3;HP=1 GT:GQ 0/1:20
…
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Hi,
First of all, thanks for the nice tool which hopefully save me some programming time for my current project. As an initial test I merged a gatk and a samtools/mpileup generated vcf file and wanted…
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Dear Dr. Lynch,
thank you for working on this code.
I have 2 populations I would like to run a sliding window Fst analysis.
The 1st population is composed of 13 individual diploid genomes with SNPs ca…
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A topic that has come up in several task teams is the need to use inheritance concepts to model class hierarchies in our data models. This has come up specifically in the G2P and annotation task teams…
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```
What steps will reproduce the problem?
1. Create a VCF file a.vcf with this line:
20 1711570 . T TG 59 PASS
DP=173;NF=0;NR=0;NRS=5;NFS=3;HP=1 GT:GQ 0/1:20
…