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Best way to obtain mcvcf files from vcf files? #23

Open biona001 opened 5 years ago

biona001 commented 5 years ago

Hello,

I have simulated some of my own reference panels in vcf format that I'd like to use as reference panels. I wish to test it on Minimac4, which means I need it to be in m3vcf format. I cannot install Minimac3 (which produces the error below after running make), and I also cannot install m3vcftools as per this issue.

What is the recommended way to obtain mcvcf files from vcf files at the moment?

For the record, I tried to clone Minimac3 onto my local machine, and after running make I get the following error:

$ make
/Library/Developer/CommandLineTools/usr/bin/make -C ../Library/libStatGenForMinimac3 --no-print-directory opt
ln -s ../samtools/bgzf.h ../include/bgzf.h
ln -s ../samtools/knetfile.h ../include/knetfile.h
ln -s ../samtools/khash.h ../include/khash.h
ln -s ../samtools/bam.h ../include/bam.h
mkdir -p obj
gcc -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/bgzf.o -c bgzf.c
gcc -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/knetfile.o -c knetfile.c
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h
ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h
ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h
ln -s ../general/BasicHash.h ../include/BasicHash.h
ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h
ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h
ln -s ../general/CharBuffer.h ../include/CharBuffer.h
ln -s ../general/Chromosome.h ../include/Chromosome.h
ln -s ../general/Cigar.h ../include/Cigar.h
ln -s ../general/CigarRoller.h ../include/CigarRoller.h
ln -s ../general/Error.h ../include/Error.h
ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h
ln -s ../general/FileType.h ../include/FileType.h
ln -s ../general/FortranFormat.h ../include/FortranFormat.h
ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h
ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h
ln -s ../general/glfHandler.h ../include/glfHandler.h
ln -s ../general/GzipFileType.h ../include/GzipFileType.h
ln -s ../general/GzipHeader.h ../include/GzipHeader.h
ln -s ../general/Hash.h ../include/Hash.h
ln -s ../general/IndexBase.h ../include/IndexBase.h
ln -s ../general/Input.h ../include/Input.h
ln -s ../general/InputFile.h ../include/InputFile.h
ln -s ../general/IntArray.h ../include/IntArray.h
ln -s ../general/IntHash.h ../include/IntHash.h
ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h
ln -s ../general/MapFunction.h ../include/MapFunction.h
ln -s ../general/MathMatrix.h ../include/MathMatrix.h
ln -s ../general/MathVector.h ../include/MathVector.h
ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h
ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h
ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h
ln -s ../general/MemoryMap.h ../include/MemoryMap.h
ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h
ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h
ln -s ../general/Parameters.h ../include/Parameters.h
ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h
ln -s ../general/Pedigree.h ../include/Pedigree.h
ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h
ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h
ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h
ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h
ln -s ../general/PhoneHome.h ../include/PhoneHome.h
ln -s ../general/QuickIndex.h ../include/QuickIndex.h
ln -s ../general/Random.h ../include/Random.h
ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h
ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h
ln -s ../general/Sort.h ../include/Sort.h
ln -s ../general/STLUtilities.h ../include/STLUtilities.h
ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h
ln -s ../general/StringAlias.h ../include/StringAlias.h
ln -s ../general/StringArray.h ../include/StringArray.h
ln -s ../general/StringBasics.h ../include/StringBasics.h
ln -s ../general/StringHash.h ../include/StringHash.h
ln -s ../general/StringMap.h ../include/StringMap.h
ln -s ../general/Tabix.h ../include/Tabix.h
ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h
ln -s ../general/Constant.h ../include/Constant.h
ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h
ln -s ../general/Generic.h ../include/Generic.h
ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h
ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h
ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h
ln -s ../general/LongHash.h ../include/LongHash.h
ln -s ../general/LongInt.h ../include/LongInt.h
ln -s ../general/MathConstant.h ../include/MathConstant.h
ln -s ../general/PackedVector.h ../include/PackedVector.h
ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h
ln -s ../general/Performance.h ../include/Performance.h
ln -s ../general/ReusableVector.h ../include/ReusableVector.h
ln -s ../general/SimpleStats.h ../include/SimpleStats.h
ln -s ../general/TrimSequence.h ../include/TrimSequence.h
ln -s ../general/UnitTest.h ../include/UnitTest.h
mkdir -p obj
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
In file included from /usr/include/Availability.h:242:0,
                 from /usr/include/stdlib.h:61,
                 from BasicHash.h:21,
                 from BasicHash.cpp:18:
/usr/include/AvailabilityInternal.h:33:18: error: missing binary operator before token "("
 #if __has_include(<AvailabilityInternalPrivate.h>)
                  ^
In file included from /usr/include/stdlib.h:61:0,
                 from BasicHash.h:21,
                 from BasicHash.cpp:18:
/usr/include/Availability.h:503:18: error: missing binary operator before token "("
 #if __has_include(<AvailabilityProhibitedInternal.h>)
                  ^
make[3]: *** [obj/BasicHash.o] Error 1
make[2]: *** [general] Error 2
make[1]: *** [../Library/libStatGenForMinimac3/libStatGen.a] Error 2
make: *** [src] Error 2
Santy-8128 commented 5 years ago

Hi Benjamin,

I think minimac3 and m3vcftools are the only two tools that can create m3vcf files. Let us try to fi the issues that you are having with installing them maybe.

Minimac3 should not be too much of a problem to figure out. Can u tell us what is the issue with installing Minimac3 that you are facing ?

In the meantime, Jonathon, do you have any suggestions with the installation of m3vcftools, seems like something to do with libstatgen.

Regards, Sayantan Das,

23andMe

On Mon, Oct 7, 2019 at 7:45 PM Benjamin Chu notifications@github.com wrote:

Hello,

I have simulated some of my own reference panels in vcf format that I'd like to use as reference panels. I wish to test it on Minimac4, which means I need it to be in m3vcf format. I cannot install Minimac3 (which appears to be depreciated), and I also cannot install m3vcftools as per this issue https://github.com/Santy-8128/m3vcftools/issues/1.

What is the recommended way to obtain m3vcf tool at the moment?

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biona001 commented 5 years ago

Thank you for the response. For the moment, I have successfully installed Minimac3 (on a linux michine) and it gets the job done. I'm inclined on closing the issue, or at least changing it to a Mac OS installation problem?

jonathonl commented 5 years ago

You can leave this open, I will look into the Mac issue when I get a chance.