nikete
commented
8 years ago This seems worth running a new revision of hhga files before we do any further changes, so to have the bug free baseline for it
On Mon, May 9, 2016 at 8:47 PM, Erik Garrison notifications@github.com wrote:
Allele support seems to be sorted reversed...
1_8276437_CT_C reference CAGTGATCC-TTTTTT hap .-. hap .-- geno .-. geno .-- sodqfXYPZi ...... 0.0 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1108:18793:19592 SodqFxYPZI ...... 0.1 0.3 0.0 60 ST-E00185:49:H5LVWCCXX:5:1112:18437:30123 SodqfXYPZI ...... 0.2 0.3 0.0 40 ST-E00185:49:H5LVWCCXX:5:1112:17219:71859 SOdqfXYPZi ...... 0.3 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1113:2725:37471 SodqfXYPZi ...... 0.4 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1118:28993:17992 SOdqfXYPZi ...... 0.5 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1120:11637:47422 SOdqfXYPZi ...... 0.6 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1123:29643:38667 SOdqfXYPZi ...... 0.7 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1123:4816:40214 SodqfXYPZI ...... 0.8 0.3 0.0 40 ST-E00185:49:H5LVWCCXX:5:1124:15616:2100 sOdqfXYPzI ...... 0.9 0.3 0.0 0 ST-E00185:49:H5LVWCCXX:5:1220:13718:51272 SodqfXYPZI ........T-...... 0.10 0.7 0.3 60 ST-E00185:49:H5LVWCCXX:5:2105:17859:22897 sOdqfXYPZI .........T...... 0.11 0.7 0.3 50 ST-E00185:49:H5LVWCCXX:5:1212:29237:25587 sOdqFxYPZI .-C..... 0.12 0.7 0.7 40 ST-E00185:49:H5LVWCCXX:5:2116:4593:21825 SodqfXYPZI .........-...... 0.13 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:2119:4664:50991 SodqfXYPZI .........-...... 0.14 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:2213:15930:16815 sOdqFxYPZI .........-...... 0.15 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:2105:17859:22897 SodqfXYPZI .........-...... 0.16 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:1221:24050:35168 sOdqfXYPZI .........-...... 0.17 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:2115:31500:11154 sOdqFxYPZI .........-...... 0.18 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:1213:2847:62225 SodqFxYPZI .........-...... 0.19 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:1115:3913:45963 sOdqFxYPZI .........-...... 0.20 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:1222:16103:8358 SodqfXYPZI .T...T...-...... 0.21 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:1116:2471:29683 sOdqFxYPZI .........-...... 0.22 1.0 0.7 60 ST-E00185:49:H5LVWCCXX:5:2210:13393:52538 sOdqFxYPZI .-C..... 1.0 0.7 0.7 40 ST-E00185:49:H5LVWCCXX:5:2116:4593:21825 sOdqFxYPZI .........--..... 1.1 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2216:8186:44082 SodqFxYPZI .........--..... 1.2 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:1109:13738:32637 SodqFxYPZI .........--..... 1.3 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2216:5415:71103 sOdqfXYPZI .........--..... 1.4 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2112:7059:38263 sODqfXYPZI .........--..... 1.5 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2112:7008:38280 soDqFxyPZi .........--..... 1.6 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2203:8744:49514 sOdqfXYPZI .........--..... 1.7 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2208:9231:62664 SodqFxYPZI .........--..... 1.8 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:2214:32414:63297 SodqFxYPZI .........--..... 1.9 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:1104:27075:56335 sOdqfXYPZI .........--..... 1.10 0.7 1.0 60 ST-E00185:49:H5LVWCCXX:5:1223:3354:17149 SodqFxYPZI ..... 8.0 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2220:3182:56863 SodqfXYPZI ..... 8.1 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2104:29694:28910 sOdqfXYPZI .... 8.2 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2202:23198:52573 SoDqFxYPZI .. 8.3 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:1109:4918:50868 SodqFxYPZI .. 8.4 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2117:30983:66901 sOdqFxYPZI . 8.5 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2211:17899:42517 AC_1:1.0 DP_1:6.0 QUAL:6.5 fermikit_1:10.0
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Allele support seems to be sorted reversed...