I am working with a tab separated file of SNPs (mummer output) and want to convert it into a variant call format (VCF). I am currently using bcftools version 1.1 to execute this with the subcommand
convert --tsv2vcf. Upon execution, there are no errors and a header of a VCF file and statistics about the conversion are displayed correctly. I am not getting any content in the VCF output though; ideally the content should be displayed for every line provided in the tab separated file. The content or "rows" are being skipping (output below). What am I doing wrong and how can I fix this to included each and every line in the initial tsv file? There is no indication as to why the rows are skipped.
Below is the command I executed, the output upon exection, and a portion of the initial text file. Any help would be appreciated.
Input File (TSV): C 4875 scaffold5-3 . C 12221 scaffold5-3 . G 17413 scaffold5-3 . C 17422 scaffold5-3 . Command Used: bcftools convert -c AA,POS,CHROM,ID -f ../OAntigen_NAg_3528-08.fasta --tsv2vcf tempFile.txt -O v -s OAntigen_3566-08_v2.fasta Output Example: ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##contig=<ID=3528-08_OAntigen_prev_NODE_11_&_NODE_49_Jul_18,length=103905> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT OAntigen_3566-08_v2.fasta Rows total: 377 Rows skipped: 377 Missing GTs: 0 Hom RR: 0 Het RA: 83 Hom AA: 0 Het AA: 294