Separate multi-allelic VCF lines to multiple rows

[d_chall]

The latest VCF formats (4.1+) allow for a single loci to cover multiple rows in the file when there are multiple alleles. The old standard of specifying multiple alleles in the same line is also valid. Unfortunately some analysis requires one standard and some the other. Are there any tools/scripts available which can take a VCF file with multiple alleles on one line and split them out to separate lines including the genotypes in the sample columns?
Thanks!

[mebbert]

Did you find a tool for this? I'm looking too.

[d_chall]

No I didn't, I ended having to write my own custom ruby script to do it.

[ekg]

I wrote something in C++ (https://github.com/ekg/vcflib/blob/m...eakmulti.cpp):

% vcfbreakmulti --help
usage: vcfbreakmulti [options] [file]

If multiple alleles are specified in a single record, break the record into
multiple lines, preserving allele-specific INFO fields.

[Elmaffo]

@ekg

I tried to compile vcflibs but I got some errors. Below the output of the make command, sorry it is in Italian but I can repeat with english language if needed.

bw
Andrea

---------------------------

elmaffo@arc-HP8200i7 ~/Scaricati/vcflib $ make
cd tabixpp && make
make[1]: ingresso nella directory "/home/elmaffo/Scaricati/vcflib/tabixpp"
make[2]: ingresso nella directory "/home/elmaffo/Scaricati/vcflib/tabixpp"
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:418:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:239:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
ranlib libtabix.a
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o
gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -lz -L. -ltabix
./libtabix.a(bgzf.o): nella funzione "deflate_block":
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:311: riferimento non definito a "deflate"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:313: riferimento non definito a "deflateEnd"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:305: riferimento non definito a "deflateInit2_"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:329: riferimento non definito a "deflateEnd"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:345: riferimento non definito a "crc32"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:346: riferimento non definito a "crc32"
./libtabix.a(bgzf.o): nella funzione "inflate_block":
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:380: riferimento non definito a "inflateInit2_"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:385: riferimento non definito a "inflate"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:391: riferimento non definito a "inflateEnd"
/home/elmaffo/Scaricati/vcflib/tabixpp/bgzf.c:387: riferimento non definito a "inflateEnd"
./libtabix.a(bedidx.o): nella funzione "ks_getuntil":
/home/elmaffo/Scaricati/vcflib/tabixpp/bedidx.c:11: riferimento non definito a "gzread"
./libtabix.a(bedidx.o): nella funzione "bed_read":
/home/elmaffo/Scaricati/vcflib/tabixpp/bedidx.c:103: riferimento non definito a "gzdopen"
./libtabix.a(bedidx.o): nella funzione "ks_getc":
/home/elmaffo/Scaricati/vcflib/tabixpp/bedidx.c:11: riferimento non definito a "gzread"
./libtabix.a(bedidx.o): nella funzione "bed_read":
/home/elmaffo/Scaricati/vcflib/tabixpp/bedidx.c:138: riferimento non definito a "gzclose"
/home/elmaffo/Scaricati/vcflib/tabixpp/bedidx.c:103: riferimento non definito a "gzopen64"
collect2: error: ld returned 1 exit status
make[2]: *** [tabix] Errore 1
make[2]: uscita dalla directory "/home/elmaffo/Scaricati/vcflib/tabixpp"
make[1]: *** [all-recur] Errore 1
make[1]: uscita dalla directory "/home/elmaffo/Scaricati/vcflib/tabixpp"
make: *** [tabixpp/tabix.o] Errore 2

[ekg]

@Andrea

Non ti preoccupare, parlo italiano.

Mi sembra che si manca zlib: http://stackoverflow.com/questions/1...late-with-zlib

Zlib e' installato nella tua sistema?

[Elmaffo]

@ekg

here is the list of Zlib-related packages on my Ubuntu 12.10 box:

Installed: zlib1g, zlib1g-dev, zlib1g:i386
not installed: zlib-bin, zlib-gst, zlib1g-dbg, zlibc,

do I need anyone of the "not installed"?

thanks
Andrea

[Elmaffo]

@ekg

Found out the issue was related to tabixcpp, as specified by guillermo-carrasco in this thread (check out the last messages in the thread):

https://github.com/ekg/tabixpp/issues/1

I edited the Makefile in the tabixpp folder as suggested in the thread. Everything compiled.

Bye

[d_chall]

Here you go

For anyone who is interested, I ended up writing a couple of scripts for splitting and merging multi-allelic lines.
They are available in the "utils" directory of the Atlas2 trunk.
http://sourceforge.net/projects/atlas2/

[mamons]

Here is another small tool to do the same thing, written in python:

https://github.com/moonso/vcf_parser