Pindel - issue with converting raw output to VCF

[casshyr]

I'm trying to use pindel2VCF.

I don't understand what the parameter "-d date" is used for.

I am using hg19 as my human reference genome. But I do not remember in particular what is the date that corresponds to the exact version of the file.


What should I put as date if I can't remember?

[Robby]

Just use any date. I think a proper vcf file needs a header line like "##fileDate=26_Jun_2014". As long as you know, that the date might be wrong and you use the vcf just for your own analysis, it should be OK.

[vwchen001]

pindel2vcf -R

Just use any date. I think a proper vcf file needs a header line like "##fileDate=26_Jun_2014". As long as you know, that the date might be wrong and you use the vcf just for your own analysis, it should be OK.

How about the reference name for hg19 human genome after -R, which is also required? Thanks!