about running variant calling ( final UnifiedGenotyper and HaplotypeCaller vcf files )
I am currently having a hard time looking for a fatal error that considerably reduces the file size of the vcf files using UnifiedGenotyper and HaplotypeCaller process. (there is a huge difference in the number of lines if I open the vcf files via typing 'vi')
From indexing a fasta file, using samtools faidx, and creating .dict file to using picard and gatk, I haven't gotten any warning or error messages. I have installed the required softwares without any error. No problem with running them, too.
The correct file sizes should be about 11MB for UG and 7MB for HC, but all I get is 7MB and 6MB each.
I attached a word document that has all my command lines in it. I've reinstalled all the necessary software (bwa, samtools, picard.tar + picard-tools.zip, gatk) and ran the whole thing twice changing the home directory of my processing. Can you please take a look at it? Thanks.