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Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically used to ligate multiple chunks of phased common variants.
Go in the test
folder and run:
phase_common --input array/target.unrelated.bcf --region 1:1-5500000 --map info/chr1.gmap.gz --output target.chunk1.bcf --thread 8
phase_common --input array/target.unrelated.bcf --region 1:4500000-10000000 --map info/chr1.gmap.gz --output target.chunk2.bcf --thread 8
echo target.chunk1.bcf > chunks.txt
echo target.chunk2.bcf >> chunks.txt
ligate --input chunks.txt --output target.phased.bcf --thread 2
The ligate program uses two threads (--thread 2) and saves the
ligated haplotypes in the output file (--output
target.phased.bcf
). Two statistics are reported while
during ligation: - Switch rate: the percentage of samples for which
haplotypes have been switched, - Avg phaseQ: the agreement of the
phasing in the overlapping region between two successive chunks of data.
We usually expect values above 80 or 90.
If some samples have been phased using pedigree information (trios/duos, option --pedigree in phase_common), you must use --pedigree here too, with the same ped file, to make sure that these haplotypes are not switched when ligated. If this is not done, haplotypes may be switched for offsprings which would make the paternal/maternal labels incorrects.
Option name | Argument | Default | Description |
---|---|---|---|
--help | NA | NA | Produces help message |
--seed | INT | 15052011 | Seed of the random number generator |
-T [ --thread ] | INT | 1 | Number of thread used |
Option name | Argument | Default | Description |
---|---|---|---|
-I [--input ] | STRING | NA | Text file containing all VCF/BCF to ligate, one file per line |
--pedigree | STRING | NA | Pedigree information (offspring father mother triplets). Really important to make sure that scaffolded samples are not switched! |
Option name | Argument | Default | Description |
---|---|---|---|
-O [--output ] | STRING | NA | Phased haplotypes in VCF/BCF format |
--no-index | STRING | NA | If specified, the output the the ligated VCF/BCF is not indexed for random access to genomic regions |
--log | STRING | NA | Log file |