Hi all,

I have a VCF file containing 190 samples from two species, with >250 000 SNPs called by Cornell's Genomics Institute. I have been able to create subsets for each of the species and filter based on FORMAT values using vcftools and vcflib. However, when I try to recompute the INFO fields, after filtering and subsetting, using vcflib's vcffixup, my NS (no. of samples) field is inaccurate, remaining constant at the total number of samples in the file (i.e. 95), even if there are samples with missing data for the SNP.

I've noticed that the records without data are represented by a './.' in the original files, but after running vcffixup they become './.:.:.:.:.'.

Is there an issue with the software? Are there other tools that I can use for this task?

I am trying to avoid using GATK as, after converting my fastq file to a 37G fasta, creating a .dict file from it using the commands here (http://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference) ran for hours before I gave up and terminated the process.

Thanks!