translate_tair8.pl Version 0.2 beta This tool translates TAIR8 to TAIR9 coordinates and bases including deletions, substitutions and insertions. Tab seperated records are read from STDIN. usage: zcat | translate_tair8.pl [-c ] [-p ] [-b ] [-o] -c : column which holds chromosomes, default 0 -p : column which holds positions, default 1 -b : column which holds bases, default 2 -o : omit insertions, only deletions and substitutions are processed. This is handy if you try to convert variant calls. Notes: Column indices are 0-based. Input files must be tab separated, line-feed (LF) terminated, and must not contain any carriage returns (CR) or empty lines. Input files may contain several chromosomes, however entries must be sorted by chromosome, position. Examples: Translate coordinates in tair8_demo.tab, chromosome is column 0, positions in column 1 and bases in column 2: $ cat tair8_demo.tab 5 26992724 A 5 26992725 G 5 26992726 A 5 26992727 T 5 26992728 C $ cat tair8_demo.tab | ./translate_tair8.pl -c0 -p1 -b2 > /tmp/tair8_demo_t9-translated.tab Same as above, but supress verbose output: $ cat tair8_demo.tab | ./translate_tair8.pl -c0 -p1 -b2 2> /dev/null Translate variant calls: $ cat Agu-1_chr5_TAIR8_example.txt Agu-1 5 26906460 G A 12 2 1 1 Agu-1 5 26906768 A - 38 5 1 1 Agu-1 5 26907254 C A 32 11 1 1 Agu-1 5 26921477 G T 23 5 1 1 Agu-1 5 26921504 A G 23 3 1 1 $ cat /tmp/Agu-1_chr5_TAIR8_example.txt \ | ./translate_tair8.pl -c1 -p2 -b3 -o \ 2> /dev/null \ > /tmp/Agu-1_chr5_TAIR8_example_tair9-translated.txt You may need to remove reference corrected positons as they are no SNPs anymore: $ awk '{if($4 != $5) print;}' variants_tair9-translated.txt Contact: Joffrey Fitz Max Planck Institute for Developmental Biology Department for Molecular Biology Tübingen, Germany