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peter huang
, …
Fan Zhang
7
9/16/20
including and excluding of sex chromosomes
Thanks Fan for the kind help! Yes, you answer the question I am interested in! Best, Peter On
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including and excluding of sex chromosomes
Thanks Fan for the kind help! Yes, you answer the question I am interested in! Best, Peter On
9/16/20
Kyoungil Min
2/26/20
VCF input when genotype information is not available
Dear Dr. Kang, Hi, I'm a graduate student from Korea, and found this tool while studying about
unread,
VCF input when genotype information is not available
Dear Dr. Kang, Hi, I'm a graduate student from Korea, and found this tool while studying about
2/26/20
Swati Goyal
,
Hyun Min Kang
4
2/12/20
Segmentation fault: 11
You need AF in the INFO field. The paper recommend at least 1000 SNPs. Individual genotypes do not
unread,
Segmentation fault: 11
You need AF in the INFO field. The paper recommend at least 1000 SNPs. Individual genotypes do not
2/12/20
VIJAY LAKHUJANI
,
Hyun Min Kang
3
1/16/20
No individual genotype information exist in the input VCF file
Please use the latest version in GitHub. See https://genome.sph.umich.edu/wiki/VerifyBamID Your VCF
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No individual genotype information exist in the input VCF file
Please use the latest version in GitHub. See https://genome.sph.umich.edu/wiki/VerifyBamID Your VCF
1/16/20
Shea Lambert
, …
Hyun Min Kang
7
3/1/19
No informative markers were found.
Your chromosome names do not match between VCF and BAM. On Fri, Mar 1, 2019 at 9:40 AM <
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No informative markers were found.
Your chromosome names do not match between VCF and BAM. On Fri, Mar 1, 2019 at 9:40 AM <
3/1/19
kiran girdhar
,
Hyun Min Kang
2
2/21/19
UNKNOWN_SM in .bestsm files
What does the header of VCF say? Is the ID included in your VCF? On Thu, Feb 21, 2019, 11:02 AM kiran
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UNKNOWN_SM in .bestsm files
What does the header of VCF say? Is the ID included in your VCF? On Thu, Feb 21, 2019, 11:02 AM kiran
2/21/19
Meghana V
1/7/19
Estimating contamination - high depth targeted panel
Hi, I am running verifybamid on high depth targeted panel data. I have around 1500 markers on the
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Estimating contamination - high depth targeted panel
Hi, I am running verifybamid on high depth targeted panel data. I have around 1500 markers on the
1/7/19
raqs...@gmail.com
,
Hyun Min Kang
4
1/2/19
Negative FREELK1 - FREELK0 for --freemix
Yes, I think that is a reasonable threshold. Obviously, the contamination wouldn't matter much if
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Negative FREELK1 - FREELK0 for --freemix
Yes, I think that is a reasonable threshold. Obviously, the contamination wouldn't matter much if
1/2/19
haroo...@gmail.com
,
Hyun Min Kang
2
12/30/18
Segmentation fault using verifyBAMID (vb1.1.3)
I guess 6000 samples are way too many and probably failing on memory allocation. Since it is RNA-seq,
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Segmentation fault using verifyBAMID (vb1.1.3)
I guess 6000 samples are way too many and probably failing on memory allocation. Since it is RNA-seq,
12/30/18
haroo...@gmail.com
,
griffanz...@gmail.com
4
12/27/18
nsufficient Available markers
The test dataset is a very small bam file which serves the purpose of validating basic functionality
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nsufficient Available markers
The test dataset is a very small bam file which serves the purpose of validating basic functionality
12/27/18
haroo...@gmail.com
, …
Rozaimi Razali
5
12/27/18
estimation per sample in the genotype file against a single BAM file
Can we use this version? verifyBamID 1.0.0 -- verify identity and purity of sequence data (c) 2010
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estimation per sample in the genotype file against a single BAM file
Can we use this version? verifyBamID 1.0.0 -- verify identity and purity of sequence data (c) 2010
12/27/18
Daekwan Seo
, …
raqs...@gmail.com
4
12/12/18
A guideline to interpret output files
Hi, I have been getting negative values (all kinds of range) for FREELK1 - FREELK0 independently of
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A guideline to interpret output files
Hi, I have been getting negative values (all kinds of range) for FREELK1 - FREELK0 independently of
12/12/18
raqs...@gmail.com
,
Hyun Min Kang
2
11/13/18
Accept several BAMs for the same VCF file
Raquel -- VCF reading time is trivial. I don't think this will be useful much and won't be
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Accept several BAMs for the same VCF file
Raquel -- VCF reading time is trivial. I don't think this will be useful much and won't be
11/13/18
Jordi Valls
,
Hyun Min Kang
4
9/5/18
Numbers of CHIPMIX and FREEMIX to contamination
I think the reason might be you used VCF with single sample, where allele frequency estimation is
unread,
Numbers of CHIPMIX and FREEMIX to contamination
I think the reason might be you used VCF with single sample, where allele frequency estimation is
9/5/18
gatla
,
Hyun Min Kang
9
9/5/18
Why IBD is very high for self and best matching individual ?
Thank you very much for taking time and clarifying it, On Wednesday, 5 September 2018 15:57:31 UTC+2,
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Why IBD is very high for self and best matching individual ?
Thank you very much for taking time and clarifying it, On Wednesday, 5 September 2018 15:57:31 UTC+2,
9/5/18
Jordi Valls
,
Hyun Min Kang
11
8/31/18
The CHIPMIX is empty
Hi Hyun, thanks for your answer, finally I get the number of CHIPMIX. The problem was the sample ID..
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The CHIPMIX is empty
Hi Hyun, thanks for your answer, finally I get the number of CHIPMIX. The problem was the sample ID..
8/31/18
Katie
, …
Hyun Min Kang
5
8/30/18
List of variants analysed/used in calculation
I believe that it is using the SNPs with at least one coverage. Hyun. On Thu, Aug 30, 2018 at 6:35 AM
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List of variants analysed/used in calculation
I believe that it is using the SNPs with at least one coverage. Hyun. On Thu, Aug 30, 2018 at 6:35 AM
8/30/18
Hyun Min Kang
8/29/18
Re: Sample swap and IBD interpretation
1. I think so. 2. I guess this might be a bug, and will look into it. 3. IBD is opposite of
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Re: Sample swap and IBD interpretation
1. I think so. 2. I guess this might be a bug, and will look into it. 3. IBD is opposite of
8/29/18
Mario Saare
, …
Hyun Min Kang
4
8/28/18
FAIL_IO: Failed to read the record size
This means that the BAM file failed to read, so it's more like a disk problem. Hyun. On Tue, Aug
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FAIL_IO: Failed to read the record size
This means that the BAM file failed to read, so it's more like a disk problem. Hyun. On Tue, Aug
8/28/18
Matthew Skirvin
, …
huilei xu
5
8/28/18
Unspecified error killing verifyBamID process
Found another thread and replied there, merge the two threads here: https://groups.google.com/d/msg/
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Unspecified error killing verifyBamID process
Found another thread and replied there, merge the two threads here: https://groups.google.com/d/msg/
8/28/18
Lavi Bharath
,
kiran girdhar
3
6/14/18
verifybamId for GRCH38 reference
Sorry, header was wrongly added here. I have converted (picard liftover) vcf to grch38 build. When I
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verifybamId for GRCH38 reference
Sorry, header was wrongly added here. I have converted (picard liftover) vcf to grch38 build. When I
6/14/18
Jo Lynne Harenza
, …
Hyun Min Kang
4
6/5/18
verifybamID on tumors?
How many cases do you have FREEMIX greater than 5% or 10%? Do you have array data for any of those
unread,
verifybamID on tumors?
How many cases do you have FREEMIX greater than 5% or 10%? Do you have array data for any of those
6/5/18
danli...@gmail.com
6/1/18
Insufficient Available markers Warning for new VerifyBamID
Hi Hyun, Thanks for your reply about the FREEMIX, I followed your suggestion to try the new version
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Insufficient Available markers Warning for new VerifyBamID
Hi Hyun, Thanks for your reply about the FREEMIX, I followed your suggestion to try the new version
6/1/18
John Blischak
, …
Hyun Min Kang
13
5/29/18
Intuitive description of freemix score
Hi Dan -- * I think it would be the best to read the paper to understand how FREEMIX works at https:/
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Intuitive description of freemix score
Hi Dan -- * I think it would be the best to read the paper to understand how FREEMIX works at https:/
5/29/18
kiran girdhar
, …
Hyun Min Kang
13
5/25/18
resolving the verifybamid results with freemix < 2% and chipmix > 10%
I would make sure first that the sample is highly contaminated. With that much contamination, you
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resolving the verifybamid results with freemix < 2% and chipmix > 10%
I would make sure first that the sample is highly contaminated. With that much contamination, you
5/25/18
kiran girdhar
5/11/18
Difference between FREEMIX and CHIPMIX
I have question on FREEMIX parameter I have this from you Hyun Min Kang "The key idea of FREEMIX
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Difference between FREEMIX and CHIPMIX
I have question on FREEMIX parameter I have this from you Hyun Min Kang "The key idea of FREEMIX
5/11/18
Robert Sicko
,
Hyun Min Kang
4
2/9/18
Estimating Contamination - Targeted Panel
When estimating FREEMIX, you can still use all 1000 genomes variants within the target region, to
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Estimating Contamination - Targeted Panel
When estimating FREEMIX, you can still use all 1000 genomes variants within the target region, to
2/9/18
Albert Vilella
,
Hyun Min Kang
2
1/15/18
Small pipeline I created to use VerifyBAMID. Does it make sense?
Your input VCF has to be from external source, not from the array-based SNP data. Hyun. On Mon, Jan
unread,
Small pipeline I created to use VerifyBAMID. Does it make sense?
Your input VCF has to be from external source, not from the array-based SNP data. Hyun. On Mon, Jan
1/15/18
Timothee Cezard
, …
Nathalie Lai
5
11/1/17
Report all samples from the genotype file
hello, Why don't I find the same fIBD when comparing Sample 1 to Sample2, and Sample 2 to Sample
unread,
Report all samples from the genotype file
hello, Why don't I find the same fIBD when comparing Sample 1 to Sample2, and Sample 2 to Sample
11/1/17
Sami A
10/22/17
Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع
موقع اليوتيوب الذي عرض فيديوهات جلسة استماع الكونجرس الأمريكي لمتابعة نشاطات غسل الأموال ونشاطات
unread,
Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع
موقع اليوتيوب الذي عرض فيديوهات جلسة استماع الكونجرس الأمريكي لمتابعة نشاطات غسل الأموال ونشاطات
10/22/17