Mega2

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This group provides support to users of the Mega2 “Manipulation Environment for Genetic Analyses” program, which is a data-handling program for facilitating genetic linkage and association analyses. Mega2 is available from http://watson.hgen.pitt.edu/register/ and Mega2 documentation is available here.

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7/1/21

Mega2: *** buffer overflow detected ***: mega2 terminated

Bug: When attempting to convert from a VCF containing 7 million variants across the chromosomes,

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Mega2: *** buffer overflow detected ***: mega2 terminated

Bug: When attempting to convert from a VCF containing 7 million variants across the chromosomes,

7/1/21

Ana Marija, Dan Weeks2

9/18/20

how to convert Plink files to Merlin format

Dear Ana, I'm sorry - we discussed and explored your report of this type of "(file "

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how to convert Plink files to Merlin format

Dear Ana, I'm sorry - we discussed and explored your report of this type of "(file "

9/18/20

6/23/20

#10:disk I/O error

Hello, I was running mega2 as in this example https://docs.google.com/viewer?a=v&pid=

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#10:disk I/O error

Hello, I was running mega2 as in this example https://docs.google.com/viewer?a=v&pid=

6/23/20

Ana Marija, Dan Weeks2

6/23/20

How to convert Plink case-control to Merlin format?

Dear Ana, While the error message is not very informative and should be improved, it looks like it is

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How to convert Plink case-control to Merlin format?

Dear Ana, While the error message is not very informative and should be improved, it looks like it is

6/23/20

Baojian Fan, Dan Weeks10

5/19/20

How to include covariates in Mega2famSKATRC

When I was importing plink binary files (ie, .bed, .bim and .fam) to mega2 v6.0.0 or v5.0.0, there is

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How to include covariates in Mega2famSKATRC

When I was importing plink binary files (ie, .bed, .bim and .fam) to mega2 v6.0.0 or v5.0.0, there is

5/19/20

Joshua Pritikin, Dan Weeks4

2/20/19

library interface?

Mega2 is GPL-2 licensed, so you are of course free to take our code and reformat it into a C++

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library interface?

Mega2 is GPL-2 licensed, so you are of course free to take our code and reformat it into a C++

2/20/19

Yann, Dan Weeks5

1/24/19

Example conversion PLINK to Merlin

[ This query to the Mega2 Google Group was answered offline a while ago, but for completeness we are

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Example conversion PLINK to Merlin

[ This query to the Mega2 Google Group was answered offline a while ago, but for completeness we are

1/24/19

Shicheng Guo, Dan Weeks3

8/22/18

read_impute_bgen2.cpp:100: error: no matching function for call to ‘BgenParserGenotypeReadHelper::get_sample_ids(BgenParserGenotypeReadHelper::genotyp

Thank you for sharing your solution. Dan

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read_impute_bgen2.cpp:100: error: no matching function for call to ‘BgenParserGenotypeReadHelper::get_sample_ids(BgenParserGenotypeReadHelper::genotyp

Thank you for sharing your solution. Dan

8/22/18

Teresa Filshtein, … Dan Weeks5

8/22/18

Mega2 install error

Mega2 compiles OK for us using g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) on a CentOS Linux release

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Mega2 install error

Mega2 compiles OK for us using g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16) on a CentOS Linux release

8/22/18

8/22/18

Mega2 version 5.0.0: 'no database' legacy mode not working

In Mega2 version 5.0.0, do not use Option 4 of the database mode menu, as the 'no database'

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Mega2 version 5.0.0: 'no database' legacy mode not working

In Mega2 version 5.0.0, do not use Option 4 of the database mode menu, as the 'no database'

8/22/18

kumardeep chaudhary, Dan Weeks2

7/9/18

Conversion of IMPUTE2 .gen format to .vcf format with dosage value (DS)

Dear Kumar, Mega2 does not currently support conversion of 3 genotype probability values to a DS

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Conversion of IMPUTE2 .gen format to .vcf format with dosage value (DS)

Dear Kumar, Mega2 does not currently support conversion of 3 genotype probability values to a DS

7/9/18

11/9/17

Our R package Mega2R is now available in CRAN

Announcement: Mega2R will let you easily bring your genetic data into R, as well as facilitates

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Our R package Mega2R is now available in CRAN

Announcement: Mega2R will let you easily bring your genetic data into R, as well as facilitates

11/9/17

Angela Parody, Dan Weeks2

10/25/17

errors "illegal affect", "disconnected", "check_ped_relations" WARNING -> Unconnected entries

Dear Angela, To treat each of the individuals as unrelated, then you need to give each of them a

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errors "illegal affect", "disconnected", "check_ped_relations" WARNING -> Unconnected entries

Dear Angela, To treat each of the individuals as unrelated, then you need to give each of them a

10/25/17

Nandita Mukhopadhyay2

8/5/15

Loop breaking and Mendel output file bugs

Correction re item 2) above: in the Mendel option, the locus file names both alleles "2",

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Loop breaking and Mendel output file bugs

Correction re item 2) above: in the Mendel option, the locus file names both alleles "2",

8/5/15

Nandita Mukhopadhyay, Dan Weeks3

8/5/15

SimWalk2 format conversion

SimWalk2 can handle letter alleles. If I take the example 'bed.*' files from the 'example

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SimWalk2 format conversion

SimWalk2 can handle letter alleles. If I take the example 'bed.*' files from the 'example

8/5/15

Jessica Perez Alquicira, Dan Weeks2

7/30/15

error 'mega2log2html.pl' may not be installed

We see that you were having problems using Mega2. Your post shows two problems. The first was

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error 'mega2log2html.pl' may not be installed

We see that you were having problems using Mega2. Your post shows two problems. The first was

7/30/15

6/13/15

Mega2 v4.8.0 released: now reads IMPUTE2 format input

We have just released a new version of Mega2, version 4.8.0, available from https://watson.hgen.pitt.

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Mega2 v4.8.0 released: now reads IMPUTE2 format input

We have just released a new version of Mega2, version 4.8.0, available from https://watson.hgen.pitt.

6/13/15

Arija, Dan Weeks3

4/2/15

segmentation fault

Thank you Dan, I will try that. Best, Arija

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segmentation fault

Thank you Dan, I will try that. Best, Arija

4/2/15

6/13/14

Mega2 v4.7.0 assumes trait is dichotomous by default when reading from a PLINK fam file.

When version 4.7.0 of Mega2 reads a PLINK file in 'ped' format, it assumes that the trait

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Mega2 v4.7.0 assumes trait is dichotomous by default when reading from a PLINK fam file.

When version 4.7.0 of Mega2 reads a PLINK file in 'ped' format, it assumes that the trait

6/13/14

11/26/13

Encountered error about more than two alleles seen for 2 bit compression

In the latest update to Mega2, we made it much more memory efficient and, in the process, set the

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Encountered error about more than two alleles seen for 2 bit compression

In the latest update to Mega2, we made it much more memory efficient and, in the process, set the

11/26/13

6/11/13

Mega2 v4.5.8: Compilation problems on Red Hat Enterprise Linux 5.9

Version 4.5.8 of Mega2 fails to compile properly on Red Hat Enterprise Linux 5.9 and CentOS 5.9. A

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Mega2 v4.5.8: Compilation problems on Red Hat Enterprise Linux 5.9

Version 4.5.8 of Mega2 fails to compile properly on Red Hat Enterprise Linux 5.9 and CentOS 5.9. A

6/11/13

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