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churchill-lab / g2gtools

Personal diploid genome creation and coordinate conversion
http://churchill-lab.github.io/g2gtools
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what vcf file to input to g2gtools v0.2.7 vcf2vci -i? indels or snps? or both? #16

Closed xiaodongpang23 closed 5 years ago

xiaodongpang23 commented 5 years ago

Based on the user guide https://g2gtools.readthedocs.io/en/latest/usage.html VCF indels is the vcf file to vcf2chain and VCF snps is for patch as follow: g2gtools vcf2chain -f ${REF} -i ${VCF_INDELS} -s ${STRAIN} -o ${STRAIN}/REF-to-${STRAIN}.chain g2gtools patch -i ${REF} -s ${STRAIN} -v ${VCF_SNPS} -o ${STRAIN}/${STRAIN}.patched.fa

However, in the g2gtools v0.27, there is no vcf2chain but only vcf2vci. So what vcf file should I input to g2gtools vcf2vci -i? indels or snps? or both?

Update the user guide to the latest version would be appreciated.

kbchoi-jax commented 5 years ago

Use both, for example, '-i -i '. See the front page of this github. There's a new link to the v0.2.x documentation.