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Feedback about challenging high-confidence GIAB calls
This form is intended to allow users of Genome in a Bottle/NIST Reference Materials an opportunity to report questionable GIAB high-confidence calls and thereby help improve our high-confidence calls in our GIAB genomes. This form is intended for letting us know about relatively small numbers of sites inside our high confidence regions that you have manually curated and believe may be incorrect. If you have many sites that would be too time-consuming to enter via this form, you can email Justin Zook (Justin 'dot' Zook 'at' nist 'dot' gov) to help find a more efficient solution. Also, feel free to email Justin with any suggestions to improve this form. You can view feedback that everyone has submitted in a spreadsheet here:
https://docs.google.com/spreadsheets/d/1kHgRLinYcnxX3-ulvijf2HrIdrQWz5R5PtxZS-_s6ZM/edit?usp=sharing
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* Indicates required question
Your name
Name, email, and institution are not required but allow us to contact you with questions. If you are making multiple entries, you can skip your email and institution in future submissions.
Your answer
Your email (if this is your first entry)
Your answer
Your Institution (if this is your first entry)
Your answer
GIAB Genome
*
HG001/NA12878
HG002/AJ Son
HG003/AJ Father
HG004/AJ Mother
HG005/Chinese son
HG006/Chinese father
HG007/Chinese mother
Reference assembly
*
GRCh37/hg19
GRCh38/hg38
Version of high-confidence calls
*
NISTv4.1
NISTv4.0
NISTv3.3.2
NISTv3.3.1
NISTv3.3
NISTv3.2.2
NISTv3.2
NISTv3.1beta
NISTv2.19
GIABv0.2
NISTv2.18
NISTv2.17
Does the GIAB call appear to be correct?
*
Yes, variant and genotype are correct
No, Variant is correct but GIAB genotype is incorrect
No, true call is missing from GIAB calls or both variant and genotype are incorrect
No, true call is homozygous reference
It is unclear
Other:
Optionally, enter the vcf line (or related vcf lines) here instead of entering chromosome, position, REF, ALT, and genotype below
Your answer
Chromosome number
Choose
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
X
Y
MT
Other (enter name before start position below)
Start Position on chromosome
Your answer
True Reference base(s)
What would typically go in the REF column of a vcf. The bases that are replaced by the ALT bases
Your answer
True Alternate base(s) - 2 alternates should be separated by a comma and no space
What would typically go in the ALT column of a VCF. The bases that replace the REF. Compound heterozygous calls should be separated by a comma
Your answer
Genotype in VCF format
0/0 (Homozygous reference)
0/1 (Heterozygous)
1/1 (Homozygous variant)
1/2 (Compound heterozygous)
Other:
Clear selection
What evidence do you have that you are correct? Be as specific as possible. Check all that apply
*
Sanger confirmation
Confirmation with second NGS method
Confirmation with high coverage sequencing with same technology as primary assay
Manual inspection of reads from your assay
Manual inspection of reads from other sequencing datasets from this genome
Evidence from long reads, linked reads, long mate-pairs, or other long-range technologies
Evidence from phasing using pedigree or long/linked reads
Other:
Required
Did you find any other variants within 50 bp of this variant?
*
Yes
No
I don't know
If yes, please give some information about the other variants and how confident you are in them.
Your answer
rs number of the variant if it is in dbSNP and you know it
Your answer
Is this a repetitive region?
No
Yes, homopolymer
Yes, tandem repeat
Other:
Clear selection
Is there any additional information about this variant or region that would be useful for us to know?
might include info about pseudogenes, CNVs, etc.
Your answer
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