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Use SnpEff to annotate wheat variations

2021/06/07

  1. Install SnpEff based on the directions here: https://pcingola.github.io/SnpEff/download/

    # Go to home dir
cd
# Download latest version
wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
# Unzip file
unzip snpEff_latest_core.zip

  2. Download the wheat annotation database (hexaploid wheat, they also have tetraploid annotations)

    cd  snpEff
java -jar snpEff.jar download Triticum_aestivum

  3. Run snpEff

    java -Xmx20g -jar /path/to/path/to/snpEff/snpEff.jar -v -stats summary.html Triticum_aestivum your.vcf.gz > your.Ta.ann.vcf

  4. Convert vcf to an variant table with annotation

    cat your.vcf.gz.Ta.ann.vcf | java -jar /path/to/snpEff/SnpSift.jar filter "( QUAL > 100 )" | /path/to/snpEff/scripts/vcfEffOnePerLine.pl | java -jar /path/to/snpEff/SnpSift.jar extractFields - CHROM POS REF ALT QUAL AC AN DP MQ "ANN[*].EFFECT" "ANN[*].GENE" "ANN[*].FEATUREID" "ANN[*].IMPACT" "ANN[*].HGVS_P" "GEN[*]" > your-ann-table.txt

  5. Convert vcf alleles from numbers to ATGC Get the python script here.

    python ./convert_vcf_calls_to_SNP_and_add_Blosum62_score.py your-ann-table.txt converted-your-ann-table.txt