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Downgrade VCF 4.2 to VCF 4.1 for viewing in IGV
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| # If you are trying to view VCF 4.2 files in IGV - you may run into issues. This function might help you. | |
| # This script will: | |
| # 1. Rename the file as version 4.1 | |
| # 2. Replace parentheses in the INFO lines (IGV doesn't like these!) | |
| function vcf_downgrade() { | |
| outfile=${1/.bcf/} | |
| outfile=${outfile/.gz/} | |
| outfile=${outfile/.vcf/} | |
| bcftools view --max-alleles 2 -O v $1 | \ | |
| sed "s/##fileformat=VCFv4.2/##fileformat=VCFv4.1/" | \ | |
| sed "s/(//" | \ | |
| sed "s/)//" | \ | |
| sed "s/,Version=\"3\">/>/" | \ | |
| bcftools view -O z > ${outfile}.dg.vcf.gz | |
| tabix ${outfile}.dg.vcf.gz | |
| } | |
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hello, please how do you parse the input vcf file using the script and generate the output vcf file with version 4.1?