Category Archives: VAT

A question regarding VAT (twoBitToFa: command not found)

Posted on by
Reply

Q1:
The psiDR is a valuable resource for my research.

In the corresponding publication (The GENCODE pseudogene resource, Pei et
al., Genome Biology, 2012), you describe in "Material & Methods:
Identification of the parents of pseudogenes and sequence similarity to
the parent" that the exons of parent and pseudogenes were used to align
them via ClustalW2.

Is it possible to provide me the alignments? That would be great.

A1:
Edit @PATH

Q2:
That is, can we run VAT (snpMapper) on a simple mutation list (as shown below)?
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO
14 30525048 . . . . . .
19 28364092 . . . . . .
2 144165461 . . . . . .
2 144224307 . . . . . .
4 98318053 . . . . . .

No rs numbers, no sample IDs and no group:sample files are present in this case, as I just wanted to run VAT for a list of somatic mutations to see if they are annotated to a coding or non-coding region.

There will be no duplicates in the list too, as I have already handled their frequency beforehand.

A2:
I will update documentation on VAT. Thanks for pointing it out to us. Regarding the input that is a non-vcf file,
just make a dummy vcf file. That is have extra columns that are tab-delimited.. Please e-mail me if you have more questions. However, bear with me as my computer just died and I am trying to get it fixed.

Question about definition of startOverlap and endOverlap in VAT

Posted on by
Reply

Q:
I have been using your variant annotation tool VAT and I have a question about what the definition is of startOverlap and endOverlap. I went through the example workflow and I have annotated another file, but I do not have any variants annotated with these types in my files. I went through your website but I could not find a listing of definitions for the terms. Thank you.

A:
These features are annotated only for indels. Essentially, when a indels affects the START of a gene or the end of a gene, it is annotated as startOverlap and end Overlap respectively. You can find extensive documentation for VAT at vat.gersteinlab.org. Please click on "Documentation" tab. Please let me know if you have any more questions.

Installing VAT

Posted on by
Reply

Q:
Thank you for offering VAT free to scientific community. A few users of our cluster requested this software to be installed on our 6000 node cluster.
But I ran into problem while trying to compile it. Hopefully you can provide some help.Thank you in advance.

I have followed your instruction on
http://vat.gersteinlab.org/documentation.php
But when I try to make vat, I got following errors. I have attached the
config.log file.:

/data/rl/vat-2.0.0> env | eg FLAGS

LDFLAGS=-L/usr/local/gsl-1.14/lib -L/usr/local/gd-2.0.35/lib
-L/usr/local/libs3-2.0/lib -L/usr/local/bios/lib
CPPFLAGS=-I/usr/local/gsl-1.14/include -I/usr/local/gd-2.0.35/include
-I/usr/local/libs3-2.0/include -I/usr/local/bios/include

/data/rl/vat-2.0.0> make
make all-recursive
make[1]: Entering directory `/gs1/users/rl/vat-2.0.0′
Making all in lib
make[2]: Entering directory `/gs1/users/rl/vat-2.0.0/lib’
GEN alloca.h
GEN configmake.h
GEN langinfo.h
GEN stdlib.h
GEN unistd.h
GEN wchar.h
GEN wctype.h
make all-recursive
make[3]: Entering directory `/gs1/users/rl/vat-2.0.0/lib’
make[4]: Entering directory `/gs1/users/rl/vat-2.0.0/lib’
CC localcharset.o
AR libgnu.a
make[4]: Leaving directory `/gs1/users/rl/vat-2.0.0/lib’
make[3]: Leaving directory `/gs1/users/rl/vat-2.0.0/lib’
make[2]: Leaving directory `/gs1/users/rl/vat-2.0.0/lib’
Making all in src
make[2]: Entering directory `/gs1/users/rl/vat-2.0.0/src’
CC vcf.o
CC util.o
CC shutil.o
CC cfio.o
CC md5.o
CC growbuffer.o
CC s3.o
AR libvat.a
CC gencode2interval.o
CCLD gencode2interval
CC interval2sequences.o
CCLD interval2sequences
CC snpMapper.o
CCLD snpMapper
CC indelMapper.o
CCLD indelMapper
CC svMapper.o
CCLD svMapper
CC genericMapper.o
CCLD genericMapper
CC vcf2images.o
CCLD vcf2images
vcf2images.o: In function `generateLegend’:
/data/rl/vat-2.0.0/src/vcf2images.c:516: undefined reference to `gdImagePng’
vcf2images.o: In function `main’:
/data/rl/vat-2.0.0/src/vcf2images.c:564: undefined reference to `gdImagePng’
collect2: ld returned 1 exit status
make[2]: *** [vcf2images] Error 1
make[2]: Leaving directory `/gs1/users/rl/vat-2.0.0/src’
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/gs1/users/rl/vat-2.0.0′
make: *** [all] Error 2
/data/rl/vat-2.0.0> echo $?

A:
Thank you for your interest in VAT. It appears that the compiler is unable to find the reference for gdImagePng, which is part of the GD library.
It is important to install and configure the GD library before installing VAT.