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churchill-lab / g2gtools

Personal diploid genome creation and coordinate conversion
http://churchill-lab.github.io/g2gtools
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convert error (key error, gtf isn't created) #17

Closed gikim0203 closed 5 years ago

gikim0203 commented 5 years ago

Using g2gtools 2.7

g2gtools vcf2vci -o HG00096.vci -f $HOME/Ensembl/GRCh38.primary_assembly.genome.fa -s HG00096 --diploid -p 14 \
 -i $VCF/ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr2.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr3.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr4.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr5.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr6.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr7.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr8.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr9.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr10.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr11.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr12.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr13.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr14.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr15.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr16.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr17.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr18.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr19.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr20.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr21.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz \
 -i $VCF/ALL.chrX.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz

g2gtools patch -i $HOME/Ensembl/GRCh38.primary_assembly.genome.fa -c HG00096.vci.gz -o HG00096.patched.fa -p 14

g2gtools transform -i HG00096.patched.fa -c HG00096.vci.gz -o HG00096.fa -p 14

g2gtools convert -i $HOME/Ensembl/gencode.v29.annotation.gtf -c HG00096.vci.gz -o HG00096.gtf

g2gtools gtf2db -i HG00096.gtf -o HG00096.gtf.db

g2gtools extract -i HG00096.fa -db HG00096.gtf.db --transcripts > HG00096.transcripts.fa

Above are the commands I used following the template script in the document page. I run into the following error at the convert step

Error Type: <class 'KeyError'> Error Value: '1' <traceback object at 0x2b2e712f2788> /anaconda3/envs/g2gtools/lib/python3.6/site-packages/g2gtools/vci.py:298

Should I be using different reference genome or annotation files?

Any help would be really appreciated.. Thank you