Replace missing gt with 0/0 and calculate AF and friends
bcftools +setGT mito_medaka.vcf.gz -- -t . -n 0 | bcftools +fill-tags - -O z -o mito_medaka_af.vcf.gz
Participant_Status.csv from ppmi website along with variant calls.
Liftover with CrossMap (https://sourceforge.net/projects/crossmap) liftOverChainFile=hg19ToHg38.over.chain.gz
head -n1 Participant_Status.csv | perl -pe 's/,/\t/g' | col_ids
head -n5 Participant_Status.csv | awk -F, '{print $1, $3}'
cat Participant_Status.csv | awk -F, '{print $3}' | sort | uniq "Early Imaging (original study participants only)" "Healthy Control" "Parkinson's Disease" "Prodromal" "SWEDD"
cat Participant_Status.csv | awk -F, '{gsub(/"/, "", $1); print $1,$3}' | egrep Healthy | awk '{print "PPMI_SI_" $1}' > ppmi_healthy
bcftools view --force-samples -U -S ppmi_healthy ppmi.feb.1.2015.liftover.vcf | bcftools +fill-tags -- > ppmi.feb.1.2015.liftover.healthy.vcf
cat Participant_Status.csv | awk -F, '{gsub(/"/, "", $1); print $1,$3}' | egrep Disease | awk '{print "PPMI_SI_" $1}' > ppmi_pd
bcftools view --force-samples -U -S ppmi_pd ppmi.feb.1.2015.liftover.vcf | bcftools +fill-tags -- > ppmi.feb.1.2015.liftover.healthy.vcf
./annotate_variation.pl --buildver hg38 --downdb seq humandb/hg38_seq ./retrieve_seq_from_fasta.pl humandb/hg38_refGene.txt -seqdir humandb/hg38_seq -format refGene -outfile humandb/hg38_refGeneMrna.fa ./annotate_variation.pl -webfrom annovar -downdb avdblist -buildver hg38 . ./annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp150 humandb/ ./annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad_exome humandb/ ./annotate_variation.pl -buildver hg38 -downdb cytoBand humandb/ ./annotate_variation.pl -buildver hg38 -downdb clinvar_20210501 humandb/ ./annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp42c humandb/ # sift etc
./convert2annovar.pl --format vcf ../dbdump.vcf > dbdump.avinput
./table_annovar.pl dbdump.avinput humandb/ -buildver hg38 -out dbdump_out -remove -protocol refGene,cytoBand,gnomad_exome,avsnp150 -operation g,r,f,f -nastring . -csvout -polish
#Nirvana
singularity exec --bind /home/:/home/ ../docker-nirvana/nirvana.sif dotnet /opt/nirvana/Nirvana.dll -c /home/refs/nirvana/Cache/GRCh38/Both -r /home/refs/nirvana/References/Homo_sapiens.GRCh38.Nirvana.dat --sd /home/refs/nirvana/SupplementaryAnnotation/GRCh38 -i dbdump.vcf -o dbdump