Example2: Calculate coverage for region of interest
java -jar covcal-1.0.5-jar-with-dependencies.jar -r
my-regions.tab -i chr1.1.bam,chr1.2.bam,chr1.3.bam,chr1.4.bam
File
my-regions.tab
should look like this:
AKT3 244013162 244013610 1
AKT3 244006247 244006764 1
AKT3 243776793 243777221 1
AKT3 243858713 243859198 1
AKT3 243708632 243709079 1
AKT3 243662865 243663268 1
AKT3 243664885 243668816 1
AKT3 243809015 243809519 1
AKT3 243736048 243736530 1
AKT3 243651355 243651932 1
AKT3 243715851 243716425 1
AKT3 243726842 243727330 1
AKT3 243800733 243801224 1
AKT3 243827894 243828365 1
AKT3 243675446 243675908 1
AKT3 244006666 244007066 1
AKT3 243778218 243778643 1
CAMK1G 209756882 209757457 1
CAMK1G 209781023 209781458 1
CAMK1G 209783016 209783454 1
CAMK1G 209778701 209779199 1
CAMK1G 209785950 209786437 1
CAMK1G 209784630 209785077 1
CAMK1G 209768120 209768600 1
CAMK1G 209782145 209782617 1
CAMK1G 209786205 209787463 1
CAMK1G 209776379 209776813 1
CAMK1G 209784957 209785741 1
CAMK1G 209779485 209779968 1
CAMK1G 209773148 209773636 1
ERRFI1 8075375 8075932 1
ERRFI1 8086038 8086573 1
ERRFI1 8075188 8075624 1
ERRFI1 8071600 8074636 1
JAK1 65310257 65310752 1
JAK1 65348780 65349338 1
JAK1 65351762 65352204 1
JAK1 65321012 65321561 1
JAK1 65300899 65301369 1
JAK1 65338873 65339386 1
JAK1 65313035 65313538 1
JAK1 65301601 65302078 1
JAK1 65311016 65311503 1
JAK1 65332369 65333071 1
JAK1 65344528 65345011 1
JAK1 65305106 65305658 1
JAK1 65306748 65307202 1
JAK1 65298726 65300520 1
JAK1 65303968 65304452 1
JAK1 65431836 65432367 1
JAK1 65312152 65312599 1
JAK1 65323159 65323642 1
JAK1 65309567 65310078 1
JAK1 65303435 65303967 1
JAK1 65306954 65307464 1
JAK1 65325608 65326125 1
JAK1 65330290 65330835 1
JAK1 65316307 65316773 1
JAK1 65334814 65335337 1
JUN 59246285 59249965 1
NRAS 115246898 115250851 1
NRAS 115259099 115259695 1
NRAS 115256241 115256779 1
NRAS 115258491 115258978 1
NRAS 115250595 115250993 1
NRAS 115252010 115252529 1
NRAS 115250972 115251455 1
PIK3CD 9770076 9770518 1
PIK3CD 9783003 9783530 1
PIK3CD 9751345 9751809 1
PIK3CD 9781639 9782098 1
PIK3CD 9781322 9781825 1
PIK3CD 9711610 9712040 1
PIK3CD 9786787 9789352 1
PIK3CD 9781853 9782391 1
PIK3CD 9780620 9781147 1
PIK3CD 9777415 9777864 1
PIK3CD 9776837 9777346 1
PIK3CD 9776318 9776857 1
PIK3CD 9779799 9780255 1
PIK3CD 9782122 9782594 1
PIK3CD 9780312 9780899 1
PIK3CD 9781001 9781486 1
PIK3CD 9782406 9782844 1
PIK3CD 9778572 9779153 1
PIK3CD 9779990 9780480 1
PIK3CD 9784154 9784659 1
PIK3CD 9783847 9784330 1
PIK3CD 9775727 9776316 1
PIK3CD 9770334 9770834 1
PIK3CD 9784682 9785174 1
PIK3CD 9775419 9776007 1
PIK3R3 46509154 46509723 1
PIK3R3 46597339 46598560 1
PIK3R3 46641720 46642330 1
PIK3R3 46543007 46543465 1
PIK3R3 46521287 46521823 1
PIK3R3 46532403 46532943 1
PIK3R3 46531548 46532031 1
PIK3R3 46511410 46511940 1
PIK3R3 46546134 46546602 1
PIK3R3 46598191 46598888 1
PIK3R3 46512043 46512477 1
PIK3R3 46527421 46527923 1
PIK3R3 46640978 46641481 1
SHC1 154939967 154940453 1
SHC1 154942328 154943403 1
SHC1 154934595 154937024 1
SHC1 154940791 154941270 1
SHC1 154938242 154938736 1
SHC1 154941067 154941549 1
SHC1 154946544 154947139 1
SHC1 154942770 154943182 1
SHC1 154941674 154942104 1
SHC1 154937839 154938437 1
SHC1 154938458 154938887 1
SHC1 154938615 154939173 1
SHC1 154940276 154940687 1
SHC1 154940500 154940913 1
SHC1 154945589 154946164 1
TGFBR3 92187332 92187881 1
TGFBR3 92223990 92224487 1
TGFBR3 92177620 92178279 1
TGFBR3 92200153 92200696 1
TGFBR3 92365014 92365434 1
TGFBR3 92181613 92182131 1
TGFBR3 92145722 92149594 1
TGFBR3 92193036 92193543 1
TGFBR3 92326848 92327381 1
TGFBR3 92351255 92351967 1
TGFBR3 92195182 92195710 1
TGFBR3 92163466 92163867 1
TGFBR3 92161049 92161516 1
TGFBR3 92174040 92174520 1
TGFBR3 92371203 92371739 1
TGFBR3 92185270 92185967 1
TGFBR3 92262664 92263208 1
TGFBR3 92181945 92182445 1
TGFBR3 92184689 92185201 1
This is a tab-delimited table, only second and third columns are of
interest (define start and stop of region).
