Make a BED file of HumVar variants with rsIds

make-humvar-snps.bed

# get HumVar
wget ftp://genetics.bwh.harvard.edu/pph2/training/humvar-2011_12.predictions.tar.gz
tar -zxvf humvar-2011_12.predictions.tar.gz

# get db snp
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz
gunzip snp138.txt.gz

# get the deleterious SNPs
grep snp138.txt -wFf <(grep rs humvar-2011_12.deleterious.pph.output | cut -f 5) \
    | cut -f 2-5 \
    | awk '{print $0"\tdeleterious"}' > humvar.deleterious.bed

# get the neutral SNPs
grep snp138.txt -wFf <(grep rs humvar-2011_12.neutral.pph.output | cut -f 5) \
    | cut -f 2-5 \
    | awk '{print $0"\tneutral"}' > humvar.neutral.bed
    
# combine the two
(echo -e "chr\tstart\tend\trsid\tclass"; sort -k1,1 -k2,2n humvar.neutral.bed  humvar.deleterious.bed) > humvar.both.bed
head humvar.both.bed