KentUtils
This is part of the Kent utilities in module kentutils-302.1-gcc-5.4.0-kbiujaa
nevertheless without the appropriate chain file.
To download the latest utilitiess, try rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
.
The most notable is liftOver from UCSC here, https://genome.ucsc.edu/cgi-bin/hgLiftOver.
Suppose we have r6-b38-A2.bed
,
#CHROM start end SNP
chr1 841851 841852 1:841852:C:T
chr1 856472 856473 1:856473:G:A
chr1 858951 858952 1:858952:G:A
chr1 859841 859842 1:859842:C:G
chr1 863420 863421 1:863421:G:A
chr1 863578 863579 1:863579:G:A
chr1 864118 864119 1:864119:T:C
chr1 866155 866156 1:866156:T:G
chr1 866280 866281 1:866281:C:T
To convert back to b37, our syntax is as follows,
liftOver r6-b38-A2.bed hg38ToHg19.over.chain.gz r6-b37-A2.bed r6-b37-A2.unlifted.bed
with r6-b37-A2.bed
containing these lines,
chr1 777231 777232 1:841852:C:T
chr1 791852 791853 1:856473:G:A
chr1 794331 794332 1:858952:G:A
chr1 795221 795222 1:859842:C:G
chr1 798800 798801 1:863421:G:A
chr1 798958 798959 1:863579:G:A
chr1 799498 799499 1:864119:T:C
chr1 801535 801536 1:866156:T:G
chr1 801660 801661 1:866281:C:T