missing data in merged vcf file

[alxcmrn]

I've noticed that missing data in my merged vcf file following genotyping are haploid ".:" while all genotypes with data are correctly diploid. Running thesed -e 's/ \.\:/ \.\/\.\:/g'line on the merged vcf file does not resolve the issue. However, using 's/.:.:.:.:.:.:.:./.\/\.:.:.:.:.:.:.:./g' does resolve ploidy of missing genotypes. Just curious as to why the line from the pipeline was not functioning.

Missing data within the raw*.vcf files is coded as a single "." without additional fields

Using vcflib ver 1.0.2 for vcfcombine.

Cheers, -Alex

[jpuritz]

sed -e 's/ \.\:/ \.\/\.\:/g' needs to have literal tabs for it to work. There may be an issue with tab character encoding.