search

DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
121 stars 41 forks source link

add additional reference for Ensembl human assembly 38 #13

Closed mforde84 closed 6 years ago

mforde84 commented 6 years ago

Hi, I would like to add this reference. idxstats shows the following:

1 248956422 5335060 0 10 133797422 2096960 0 11 135086622 3007088 0 12 133275309 2220636 0 13 114364328 1559146 0 14 107043718 3120738 0 15 101991189 1346306 0 16 90338345 1713268 0 17 83257441 2357610 0 18 80373285 618100 0 19 58617616 1441954 0 2 242193529 3693058 0 20 64444167 1508904 0 21 46709983 22438086 0 22 50818468 703842 0 3 198295559 3085302 0 4 190214555 1500350 0 5 181538259 2348104 0 6 170805979 3106762 0 7 159345973 2917186 0 8 145138636 2210556 0 9 138394717 2446060 0 MT 16569 147374 0 X 156040895 1218960 0 Y 57227415 37718 0 KI270728.1 1872759 1868 0 KI270727.1 448248 514 0 KI270442.1 392061 232 0 KI270729.1 280839 170 0 GL000225.1 211173 228 0 KI270743.1 210658 322 0 GL000008.2 209709 656 0 GL000009.2 201709 1044 0 KI270747.1 198735 254 0 KI270722.1 194050 82 0 GL000194.1 191469 1550 0 KI270742.1 186739 1588 0 GL000205.2 185591 2370 0 GL000195.1 182896 9600 0 KI270736.1 181920 44 0 KI270733.1 179772 9788058 0 GL000224.1 179693 1092 0 GL000219.1 179198 1092 0 KI270719.1 176845 2440 0 GL000216.2 176608 206 0 KI270712.1 176043 1692 0 KI270706.1 175055 1674 0 KI270725.1 172810 316 0 KI270744.1 168472 794 0 KI270734.1 165050 434 0 GL000213.1 164239 260 0 GL000220.1 161802 9727154 0 KI270715.1 161471 22 0 GL000218.1 161147 3756 0 KI270749.1 158759 206 0 KI270741.1 157432 48 0 GL000221.1 155397 1372 0 KI270716.1 153799 32 0 KI270731.1 150754 414 0 KI270751.1 150742 244 0 KI270750.1 148850 30 0 KI270519.1 138126 18 0 GL000214.1 137718 254 0 KI270708.1 127682 76 0 KI270730.1 112551 12 0 KI270438.1 112505 78 0 KI270737.1 103838 42 0 KI270721.1 100316 1604 0 KI270738.1 99375 70 0 KI270748.1 93321 624 0 KI270435.1 92983 34 0 GL000208.1 92689 30 0 KI270538.1 91309 4 0 KI270756.1 79590 6 0 KI270739.1 73985 4 0 KI270757.1 71251 0 0 KI270709.1 66860 34 0 KI270746.1 66486 154 0 KI270753.1 62944 22 0 KI270589.1 44474 2 0 KI270726.1 43739 24 0 KI270735.1 42811 32 0 KI270711.1 42210 5314 0 KI270745.1 41891 2244 0 KI270714.1 41717 516 0 KI270732.1 41543 20 0 KI270713.1 40745 185894 0 KI270754.1 40191 4 0 KI270710.1 40176 0 0 KI270717.1 40062 1294 0 KI270724.1 39555 6 0 KI270720.1 39050 116 0 KI270723.1 38115 14 0 KI270718.1 38054 966 0 KI270317.1 37690 0 0 KI270740.1 37240 0 0 KI270755.1 36723 54 0 KI270707.1 32032 104 0 KI270579.1 31033 0 0 KI270752.1 27745 2 0 KI270512.1 22689 0 0 KI270322.1 21476 0 0 GL000226.1 15008 0 0 KI270311.1 12399 0 0 KI270366.1 8320 0 0 KI270511.1 8127 0 0 KI270448.1 7992 0 0 KI270521.1 7642 0 0 KI270581.1 7046 0 0 KI270582.1 6504 4 0 KI270515.1 6361 0 0 KI270588.1 6158 0 0 KI270591.1 5796 0 0 KI270522.1 5674 0 0 KI270507.1 5353 0 0 KI270590.1 4685 0 0 KI270584.1 4513 0 0 KI270320.1 4416 0 0 KI270382.1 4215 2 0 KI270468.1 4055 0 0 KI270467.1 3920 16 0 KI270362.1 3530 0 0 KI270517.1 3253 0 0 KI270593.1 3041 0 0 KI270528.1 2983 0 0 KI270587.1 2969 0 0 KI270364.1 2855 0 0 KI270371.1 2805 0 0 KI270333.1 2699 0 0 KI270374.1 2656 0 0 KI270411.1 2646 0 0 KI270414.1 2489 0 0 KI270510.1 2415 0 0 KI270390.1 2387 0 0 KI270375.1 2378 0 0 KI270420.1 2321 0 0 KI270509.1 2318 0 0 KI270315.1 2276 0 0 KI270302.1 2274 4 0 KI270518.1 2186 0 0 KI270530.1 2168 0 0 KI270304.1 2165 0 0 KI270418.1 2145 0 0 KI270424.1 2140 0 0 KI270417.1 2043 0 0 KI270508.1 1951 0 0 KI270303.1 1942 0 0 KI270381.1 1930 0 0 KI270529.1 1899 0 0 KI270425.1 1884 0 0 KI270396.1 1880 0 0 KI270363.1 1803 6 0 KI270386.1 1788 0 0 KI270465.1 1774 0 0 KI270383.1 1750 0 0 KI270384.1 1658 0 0 KI270330.1 1652 20 0 KI270372.1 1650 0 0 KI270548.1 1599 0 0 KI270580.1 1553 6 0 KI270387.1 1537 0 0 KI270391.1 1484 0 0 KI270305.1 1472 0 0 KI270373.1 1451 0 0 KI270422.1 1445 0 0 KI270316.1 1444 0 0 KI270340.1 1428 0 0 KI270338.1 1428 0 0 KI270583.1 1400 0 0 KI270334.1 1368 0 0 KI270429.1 1361 0 0 KI270393.1 1308 0 0 KI270516.1 1300 0 0 KI270389.1 1298 0 0 KI270466.1 1233 12 0 KI270388.1 1216 0 0 KI270544.1 1202 0 0 KI270310.1 1201 0 0 KI270412.1 1179 0 0 KI270395.1 1143 0 0 KI270376.1 1136 0 0 KI270337.1 1121 0 0 KI270335.1 1048 0 0 KI270378.1 1048 0 0 KI270379.1 1045 2 0 KI270329.1 1040 0 0 KI270419.1 1029 0 0 KI270336.1 1026 0 0 KI270312.1 998 0 0 KI270539.1 993 4 0 KI270385.1 990 0 0 KI270423.1 981 0 0 KI270392.1 971 0 0 KI270394.1 970 0 0

however I'm not entirely sure how to format the knownReferences file.

Thanks for the help, Martin

AlexanderDilthey commented 6 years ago

Hi Martin,

I've added a reference file. You can add it by doing a 'git pull' in your installation directory. Can you give it a try?

Just to confirm: I couldn't identify any alternative MHC or HLA contigs -- correct?

Cheers,

Alex