Combine candidate gene evidence from multiple sources
Reference genomes
# in csh
tree /rsstu/users/r/rrellan/sara/ref
# /rsstu/users/r/rrellan/sara/ref
# ├── B73_RefGen_v2.fa
# ├── B73_RefGen_v2.fa.fai
# ├── Zm-B73-REFERENCE-GRAMENE-4.0.fa
# ├── Zm-B73-REFERENCE-GRAMENE-4.0.fa.fai
# ├── Zm-B73-REFERENCE-NAM-5.0.fa
# └── Zm-B73-REFERENCE-NAM-5.0.fa.fai
As there is no v2 to v5 chainfile, that liftover must be done in two steps v2 -> v4 and v4 -> v5
# in csh
tree /rsstu/users/r/rrellan/sara/ZeaGEA/results
# /rsstu/users/r/rrellan/sara/ZeaGEA/results
# ├── glm_20181019
# │ ├── GLM_Q28_site # GWAS pvalues AGPv2 corrected with K=28 subpopulations in ADMIXTURE
# │ └── GLM_site # GWAS pvalues AGPv2 no correction for kinship or population structure
# └── pcadapt
# ├── AGPv2_to_B73_RefGen_v4.chain
# ├── B73_RefGen_v2_Chr.bed
# ├── pcadapt_corrected.Rimage # PCAdapt pvalues AGPv2
# └── PCAdapt_v4.RDS # PCAdapt pvalues AGPv4
B73_RefGen_v2_Chr.bed BED file is built like:
# in csh
# activate conda environment for samtools
conda activate /usr/local/usrapps/maize/sorghum/conda/envs/snakemake-tutorial
set ref=/rsstu/users/r/rrellan/sara/ref
cd $ref
wget https://ftp.maizegdb.org/MaizeGDB/FTP/B73_RefGen_v2/B73_RefGen_v2.fa.gz
gunzip B73_RefGen_v2.fa.gz
samtools faidx B73_RefGen_v2.fa
set pcadapt=/rsstu/users/r/rrellan/sara/ZeaGEA/results/pcadapt
cd $pcadapt
head -n 10 $ref/B73_RefGen_v2.fa.fai | awk 'BEGIN {FS="\t"}; {gsub("Chr", "", $1); gsub(":.*", "", $1); print $1 FS "0" FS $2 FS "ws"}' | sort -k1,1n > B73_RefGen_v2_Chr.bed
Chain files (see specs) downloaded from the MaizeGDB ftp site won't be read by R unless spaces are replaced by tabs:
# in csh
wget "http://ftp.gramene.org/CURRENT_RELEASE/assembly_chain/zea_mays/AGPv3_to_B73_RefGen_v4.chain.gz"
gunzip AGPv3_to_B73_RefGen_v4.chain.gz
perl -i -pe ' if ( $_ !~ /chain/) {s/ +/\t/g}' AGPv3_to_B73_RefGen_v4.chain
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PBE scores (these are not p-values)
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Differential expression in +P -P experiments