Hi,
I'm currently trying to convert a vcf to smc format, running the line of code below on smcpp 1.15.5, installed via conda. (I realize that conda is not supported anymore, but I'm limited in what I can install to my working machine, and currently do not have docker as an option. In the note previously released about switching from conda to docker, the main complaint seemed to be about package resolution and install times, neither of which seemed to be an issue in my installation.)
The output is as follows:
smc++ vcf2smc: error: the following arguments are required: pop1
I'd like to specify FRANCE as a population, but it doesn't seem to recognize that, or any variant string (FR, etc...) as a pop1 argument. I haven't seen a population tag in the VCF documentation, so I don't believe I'm inputting the wrong value, but I'm unsure why it's not being parsed.
Hi, I'm currently trying to convert a vcf to smc format, running the line of code below on smcpp 1.15.5, installed via conda. (I realize that conda is not supported anymore, but I'm limited in what I can install to my working machine, and currently do not have docker as an option. In the note previously released about switching from conda to docker, the main complaint seemed to be about package resolution and install times, neither of which seemed to be an issue in my installation.)
smc++ vcf2smc --cores 10 -d FR1 FR1_rawSNPs-filt.vcf VFFE01007679.1.smc.gz VFFE01007679.1 FRANCE:FR1The output is as follows:
smc++ vcf2smc: error: the following arguments are required: pop1I'd like to specify FRANCE as a population, but it doesn't seem to recognize that, or any variant string (FR, etc...) as a pop1 argument. I haven't seen a population tag in the VCF documentation, so I don't believe I'm inputting the wrong value, but I'm unsure why it's not being parsed.