Statistical analysis of a whole exome VCF file
I have a VCF file for a whole-exome sequence dataset generated by the agilent 1.1 capture kit.
The genome coordinates are GRCh37.
If I wanted to a case-control burden test on every gene in the dataset what steps would I need to follow?
- how do I get a complete and unique list of genes to run the test on?
- how do I subset just the variants in the exons of these genes?
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WouterDeCoster
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adam.waring •
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adam.waring •
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Below is some code I used a while ago to do something similar, but not on a whole exome scale.
java -Xmx4g -jar $SNPEFF -c $SNPEFF_config GRCh37.75 yourfile.vcf > yourfile_annotated.vcf
vcftools --vcf yourfile_annotated.vcf --get-INFO ANN --stdout | \
cut -f5 | tr ',' '\n' | cut -f4 -d'|' | grep -v -w 'ANN' | sort -u | \
parallel -j6 'cat <(grep '^#' yourfile_annotated.vcf) <(grep -v '^#' yourfile_annotated.vcf | grep -w {}) > {}.split.vcf'
I hope this can put you in the right direction.
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