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Old 06-15-2011, 05:42 AM   #1
gao
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Location: china

Join Date: Jun 2011
Posts: 1
Default how to building vcftools executable ?

Hello all, I want to create the vcftools executable.when I type the commod"make",it appears that :
make[1]: Entering directory `/ifs1/AE/xxx/program_test/xxx/vcftools_0.1.4a/cpp'
g++ -O2 -Wall -Wextra vcftools.cpp vcf_file.cpp vcf_entry.cpp vcf_entry_getters.cpp vcf_entry_setters.cpp vcf_file_filters.cpp vcf_file_output.cpp vcf_file_format_convert.cpp vcf_file_diff.cpp parameters.cpp output_log.cpp -o vcftools -lz
g++: too many input files
make[1]: *** [vcftools] Error 1
make[1]: Leaving directory `/ifs1/AE/dongfangshuai/program_test/gao/vcftools_0.1.4a/cpp'
/bin/sh: line 0: cd: perl: No such file or directory
make: *** [install] Error 1

how can I install the vcftools? how can I solve the problem? thank you very much!!
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Old 08-10-2014, 08:48 PM   #2
kurban910
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Location: urumqi

Join Date: Jul 2014
Posts: 58
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i tried to install Vcftools according to http://vcftools.sourceforge.net/examples.html . and when i do make it's terminal results showed this:
Code:
[email protected]:~/Downloads/vcftools_0.1.12b$ make
make[1]: Entering directory `/home/kurban/Downloads/vcftools_0.1.12b/cpp'
g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcftools.cpp -o vcftools.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcftools.cpp > vcftools.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  bcf_file.cpp -o bcf_file.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  bcf_file.cpp > bcf_file.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcf_file.cpp -o vcf_file.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcf_file.cpp > vcf_file.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file.cpp -o variant_file.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file.cpp > variant_file.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  header.cpp -o header.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  header.cpp > header.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  bcf_entry.cpp -o bcf_entry.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  bcf_entry.cpp > bcf_entry.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcf_entry.cpp -o vcf_entry.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcf_entry.cpp > vcf_entry.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry.cpp -o entry.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry.cpp > entry.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry_getters.cpp -o entry_getters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry_getters.cpp > entry_getters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry_setters.cpp -o entry_setters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry_setters.cpp > entry_setters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  vcf_entry_setters.cpp -o vcf_entry_setters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  vcf_entry_setters.cpp > vcf_entry_setters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  bcf_entry_setters.cpp -o bcf_entry_setters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  bcf_entry_setters.cpp > bcf_entry_setters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  entry_filters.cpp -o entry_filters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  entry_filters.cpp > entry_filters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file_filters.cpp -o variant_file_filters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file_filters.cpp > variant_file_filters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file_output.cpp -o variant_file_output.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file_output.cpp > variant_file_output.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  parameters.cpp -o parameters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  parameters.cpp > parameters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file_format_convert.cpp -o variant_file_format_convert.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file_format_convert.cpp > variant_file_format_convert.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  variant_file_diff.cpp -o variant_file_diff.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  variant_file_diff.cpp > variant_file_diff.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64  output_log.cpp -o output_log.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  output_log.cpp > output_log.d
gcc -O2 -m64 -O2 -D_FILE_OFFSET_BITS=64   -c -o bgzf.o bgzf.c
bgzf.c: In function ‘bgzf_check_EOF’:
bgzf.c:622:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
g++ -c -O2 -D_FILE_OFFSET_BITS=64  gamma.cpp -o gamma.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64  gamma.cpp > gamma.d
g++ -O2 -D_FILE_OFFSET_BITS=64  vcftools.o bcf_file.o vcf_file.o variant_file.o header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o -o vcftools -lz 
cp /home/kurban/Downloads/vcftools_0.1.12b/cpp/vcftools /home/kurban/Downloads/vcftools_0.1.12b//bin/vcftools
make[1]: Leaving directory `/home/kurban/Downloads/vcftools_0.1.12b/cpp'
make[1]: Entering directory `/home/kurban/Downloads/vcftools_0.1.12b/perl'
make[1]: Leaving directory `/home/kurban/Downloads/vcftools_0.1.12b/perl'
then i entered this in the terminal it showed this:
Code:
[email protected]:~/Downloads/vcftools_0.1.12b$ vcftools --vcf input_file.vcf --remove-indels --recode --recode-INFO-all --out SNPs_only
The program 'vcftools' is currently not installed.  You can install it by typing:
sudo apt-get install vcftools
[email protected]:~/Downloads/vcftools_0.1.12b$ cd
[email protected]:~$ vcftools
The program 'vcftools' is currently not installed.  You can install it by typing:
sudo apt-get install vcftools
i know if i installed it by typing sudo apt-get install vcftools, it would have been more easy. but i wanna use this version i am trying to install here. and i believe i just installed it. but i may missed something here.so could anyone give some tips?
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Old 08-10-2014, 10:54 PM   #3
WhatsOEver
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Location: Germany

Join Date: Apr 2012
Posts: 215
Default

it looks properly installed.
i think you just not have it in your path.
Try "./vcftools" in your vcftools folder. Without the "./" only the path will be searched for the program, no matter in which folder you are in.
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Old 08-11-2014, 12:20 AM   #4
Cytosine
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Location: Belgium

Join Date: Mar 2014
Posts: 22
Default

You did compile it successfully. Now you need to specify the correct path to it if you want to use it.

You can't go wrong with a fullpath name:

/home/kurban/Downloads/vcftools_0.1.12b/cpp/vcftools

You can use that from anywhere...


If you want to use it witout the fullpath name, then you need to add it to your $PATH in your current session, or have it loaded into that variable each time by a startup script like .profile or .bashrc
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Old 08-11-2014, 04:06 AM   #5
kurban910
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Location: urumqi

Join Date: Jul 2014
Posts: 58
Default

thank you guys, yes ,it was really a problem of path.
and through the vcftools i got a file(my.var-final.vcf 27 MB) which contain in formation of SNPs and indels:

##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) tha
n in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples
.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT my-sorted.bam
comp904_c0_seq1 30 . G T 73.5 . DP=4;VDB=0.0014;AF1=1;AC1=2;DP4=0,0,4,0;MQ=60;FQ=-39 GT:PL:GQ 1/1:106,
12,0:21
comp904_c0_seq1 37 . C T 52 . DP=4;VDB=0.0014;AF1=1;AC1=2;DP4=0,0,3,0;MQ=60;FQ=-36 GT:PL:GQ 1/1:84,9
,0:16
comp904_c0_seq1 41 . A T 64.3 . DP=6;VDB=0.0020;AF1=1;AC1=2;DP4=0,0,5,0;MQ=60;FQ=-42 GT:PL:GQ 1/1:97,1
5,0:27
comp904_c0_seq1 74 . A G 4.77 . DP=21;VDB=0.0147;AF1=0.4999;AC1=1;DP4=10,5,3,1;MQ=60;FQ=6.99;PV4=1,1.2e-06,1,1
GT:PL:GQ 0/1:33,0,255:33
comp904_c0_seq1 133 . G T 137 . DP=36;VDB=0.0404;AF1=0.5;AC1=1;DP4=2,3,19,10;MQ=60;FQ=33;PV4=0.35,1.6e-09,1,1
GT:PL:GQ 0/1:167,0,60:63


this there any way to summarize this variation information, like some tools, scripts or something?
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