tsv2vcf
Format
cg tsv2vcf ?options? ?infile? ?outfile?
Summary
Converts data in genomecomb tab-separated variant format (tsv) to vcf.
Description
cg tsv2vcf converts a genomecomb tab-separated variant file (tsv) to a vcf. If metadata is present in the tsv
file (in the genomecomb metadata format), it will be used for
creating the vcf header. If the metadata is not present, A number of
default descriptions for the fieldnames are used to create the header
(these are based on the gatk(h), samtools, etc. variantcallers) The
commands needs the genomic reference sequence, which can be given
directly using the -refseq option or indirectly using -dbdir.
Arguments
- infile
- file to be converted, if not given, uses stdin. File may be
compressed.
- outfile
- write results to outfile, if not given, uses stdout
Options
- -split 0/1
- tsv files usually have all variants on separate lines. cg
tsv2vcf will by default merge variants that start at the same
position (as usual in the vcf format). Using -split 1, will put
these on separate lines as well
- -refseq refseq
- genomic reference sequence
- -dbdir dbdir
- dbdir containing reference genomes databases, used to find
the genomic reference
- -sample samplename
- For single sample tsv files (not multicoompar) the samplename
that will be used in the vcf file can be given using this option.
If not given, it will try to find the samplename in the file
(metadata), or base it on the filename
Category
Format Conversion