Broad Viral Tool Users

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This site is for users of computational tools released by the Broad Institute's Viral Genomics Group to obtain feedback from other users on their use and to report bugs.

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nagaraju madikonda

4/1/19

Viral News | Viral Information

Viral Information is work as channel to provide viral news, trending news, latest information to the

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Viral News | Viral Information

Viral Information is work as channel to provide viral news, trending news, latest information to the

4/1/19

11/13/17

Segmentation fault (core dumped) from athlates

Hi, I tried to run Athlates on some BAM files that I downloaded from the UCSC database. However, I

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Segmentation fault (core dumped) from athlates

Hi, I tried to run Athlates on some BAM files that I downloaded from the UCSC database. However, I

11/13/17

10/6/17

Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea

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Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع

YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea

10/6/17

8/30/17

--Hi, just a question: what is the difference between mvicuna and vicuna (https://www.broadinstitute.

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--Hi, just a question: what is the difference between mvicuna and vicuna (https://www.broadinstitute.

8/30/17

Guinevere Queenie Lee

5/11/17

RC454 samToQlx.pl giving empty qlx

Please help. I'm using macOS Sierra. Question 1. These lines successfully generated a qlx file

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RC454 samToQlx.pl giving empty qlx

Please help. I'm using macOS Sierra. Question 1. These lines successfully generated a qlx file

5/11/17

bram.v...@gmail.com, … Clifford Beall8

4/24/17

VPhaserII installation on Mac OSX

Thanks, I found I could get it to compile on Linux with that #include <climits> hack, so I won

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VPhaserII installation on Mac OSX

Thanks, I found I could get it to compile on Linux with that #include <climits> hack, so I won

4/24/17

Konstantin Chukreev

1/25/17

V-phaser Strand bias p-value >1

Hello! I ran V-phaser for my .bam file and got very strange results (here's some of the lines

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V-phaser Strand bias p-value >1

Hello! I ran V-phaser for my .bam file and got very strange results (here's some of the lines

1/25/17

Andrew Oler, … Ekaterina Esaulova20

3/14/16

ATHLATES producing empty *typing.txt output

Hello, I'm trying to use Athlates for typing HLA class II. I decided to test my pipeline on HLA

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ATHLATES producing empty *typing.txt output

Hello, I'm trying to use Athlates for typing HLA class II. I decided to test my pipeline on HLA

3/14/16

Bede Constantinides, Christopher Tomkins-Tinch2

2/18/16

Issues with staticallly linked binary from GitHub viral-ngs repo

Sorry to hear you've hit a snag. If you're looking for only v-phaser2, you might try the

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Issues with staticallly linked binary from GitHub viral-ngs repo

Sorry to hear you've hit a snag. If you're looking for only v-phaser2, you might try the

2/18/16

Dan Depledge, Daniel Park2

2/1/16

Problems using V-FAT for large DNA viruses

Hi Dan, I've also recently tried to use V-FAT on viruses from the herpes family and it fails to

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Problems using V-FAT for large DNA viruses

Hi Dan, I've also recently tried to use V-FAT on viruses from the herpes family and it fails to

2/1/16

2/1/16

Update on the Broad Viral Group

Hi Broad viral tool users, I'm newish to this list and this is my first time posting, but I

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Update on the Broad Viral Group

Hi Broad viral tool users, I'm newish to this list and this is my first time posting, but I

2/1/16

Sean Brimer, Dave La4

1/29/16

VICUNA Compiling issue, NCBI Toolkit v12, 64bit Ubuntu 14.01 LTS

Hi Dave, I'm so sorry for the late reply, in short I did not and moved on. There is a pre-

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VICUNA Compiling issue, NCBI Toolkit v12, 64bit Ubuntu 14.01 LTS

Hi Dave, I'm so sorry for the late reply, in short I did not and moved on. There is a pre-

1/29/16

Curtis Hendrickson (Campus), HONG KAI LEE2

11/28/15

VAnalysis crashes: Contig::create_profile p2 SC failed

This happens to some of my fastq files Rebuilding fastq files using bcl2fastq-v2.16 resolved my

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VAnalysis crashes: Contig::create_profile p2 SC failed

This happens to some of my fastq files Rebuilding fastq files using bcl2fastq-v2.16 resolved my

11/28/15

Daniel Eriksson, bmp1...@student.lu.se3

11/2/15

Update hlall.fa or hla.clean.fasta

Yes, this solves the problem. Thank you. It seemed to me that some, a few, nuc/gen sequences are

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Update hlall.fa or hla.clean.fasta

Yes, this solves the problem. Thank you. It seemed to me that some, a few, nuc/gen sequences are

11/2/15

8/19/15

Hai all Please explain the difference between,, VICUNA outputs,, contig.fasta and contig.lfv.fasta

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Hai all Please explain the difference between,, VICUNA outputs,, contig.fasta and contig.lfv.fasta

8/19/15

8/18/15

VPhaser2 FDR Question

Hi, We have run VPhaser2 on an Illumina high-depth data set to look at minority variants. We observe

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VPhaser2 FDR Question

Hi, We have run VPhaser2 on an Illumina high-depth data set to look at minority variants. We observe

8/18/15

Kathryn Edenborough, … Daniele Swetnam4

7/18/15

V Phaser-2 Compilation Errors

I'm having the same problem. Has any one fixed it out? On Friday, May 29, 2015 at 7:40:50 AM UTC-

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V Phaser-2 Compilation Errors

I'm having the same problem. Has any one fixed it out? On Friday, May 29, 2015 at 7:40:50 AM UTC-

7/18/15

michael.pa...@gmail.com

7/17/15

V-Phaser-2 Error: can't open file /V4528_assembly.0.499.region

Note, I do not have root access on my machine. Latest version of V-Phaser2 from broad's site. $

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V-Phaser-2 Error: can't open file /V4528_assembly.0.499.region

Note, I do not have root access on my machine. Latest version of V-Phaser2 from broad's site. $

7/17/15

RG, … Javier Perez Florido9

5/27/15

Meaning of V-Phaser2 output, and conversion for V profiler problem

Dear Xiao, Could you please attache also the script dependence named ntfreq_raw_all.pl which is used

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Meaning of V-Phaser2 output, and conversion for V profiler problem

Dear Xiao, Could you please attache also the script dependence named ntfreq_raw_all.pl which is used

5/27/15

Gideon Mordecai, … gludish5

5/16/15

VICUNA analysis questions. Visualising variation?

Hi David, Yep vicuna outputs consensus contigs in fasta format which you can scaffold into full

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VICUNA analysis questions. Visualising variation?

Hi David, Yep vicuna outputs consensus contigs in fasta format which you can scaffold into full

5/16/15

Jacob Hurst, … gludish6

5/15/15

Vicuna, possible to release executables?

Any chance of providing an executable that will run on Mac OSX? Many potential Vicuna users do not

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Vicuna, possible to release executables?

Any chance of providing an executable that will run on Mac OSX? Many potential Vicuna users do not

5/15/15

5/12/15

omp.h file not found

Hello, I've attached the error message I get when compiling Vicuna. It seems to be looking for

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omp.h file not found

Hello, I've attached the error message I get when compiling Vicuna. It seems to be looking for

5/12/15

Irwin Jungreis2

2/19/15

V-Phaser 2 p-value computation is unstable

I also note that on other runs some of the differing p-values are interesting. For example, -3.105e+

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V-Phaser 2 p-value computation is unstable

I also note that on other runs some of the differing p-values are interesting. For example, -3.105e+

2/19/15

AA, … Javier Perez Florido4

1/22/15

Vphaser2 error when running on bam file created by Stampy

Dear AA and Xiao, Have you fixed this problem? I've run vphaser-2 through a set of several BAMs

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Vphaser2 error when running on bam file created by Stampy

Dear AA and Xiao, Have you fixed this problem? I've run vphaser-2 through a set of several BAMs

1/22/15

bram.v...@gmail.com

12/3/14

samToQlx.pl mystery error

Hi all, I've been reading through this forum and elsewhere trying to figure out what is going

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samToQlx.pl mystery error

Hi all, I've been reading through this forum and elsewhere trying to figure out what is going

12/3/14

Louis Letourneau

11/7/14

ATHLATES and Mosaik

I was wondering if in the docs the -om option is missing in the description of how to use Mosaik with

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ATHLATES and Mosaik

I was wondering if in the docs the -om option is missing in the description of how to use Mosaik with

11/7/14

10/17/14

ATHLATES different results with BWA-mem vs BWA-aln + sampe

Hello, If I run an identical script on identical input files and references, switching only my use of

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ATHLATES different results with BWA-mem vs BWA-aln + sampe

Hello, If I run an identical script on identical input files and references, switching only my use of

10/17/14

10/1/14

Speeding up Vphaser2

Yes, its 96x1.5 so I guess it makes sense. I can try the other way of splitting the core usage.

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Speeding up Vphaser2

Yes, its 96x1.5 so I guess it makes sense. I can try the other way of splitting the core usage.

10/1/14

Ben Woodcroft, Adrian Pelin2

9/18/14

Compilation problem with VPhaser-2-02112013

Even after reading this and the mentioned link I still had trouble compiling. I am suprised this hasn

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Compilation problem with VPhaser-2-02112013

Even after reading this and the mentioned link I still had trouble compiling. I am suprised this hasn

9/18/14

Hung-Ying Lin, Fielfluff2

8/26/14

RC454 error message: ERROR getQualAtPos, BAC1.R1.frag1-10006/1 208 >= 0

Hi Hung Ying, I had a similar problem to you but my warnings were a little different (the variables $

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RC454 error message: ERROR getQualAtPos, BAC1.R1.frag1-10006/1 208 >= 0

Hi Hung Ying, I had a similar problem to you but my warnings were a little different (the variables $

8/26/14

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