diff --git a/testCrypt.txt b/testCrypt.txt new file mode 100644 index 0000000..6733f46 --- /dev/null +++ b/testCrypt.txt @@ -0,0 +1,208 @@ +gene varID +NF1 NM_000267:c.1000del +NF1 NM_000267:c.1007_1008delinsAA +NF1 NM_000267:c.1007G>A +NF1 NM_000267:c.1008G>A +NF1 NM_000267:c.1016del +NF1 NM_000267:c.1018_1031del +NF1 NM_000267:c.1019_1020del +NF1 NM_000267:c.1020dup +NF1 NM_000267:c.1021_1022del +NF1 NM_000267:c.1021_1031del +NF1 NM_000267:c.1022dup +NF1 NM_000267:c.1039C>T +NF1 NM_000267:c.1049dup +NF1 NM_000267:c.1061del +NF1 NM_000267:c.1062+1G>A +NF1 NM_000267:c.1062+3A>G +NF1 NM_000267:c.1062G>A +NF1 NM_000267:c.1063-13G>A +NF1 NM_000267:c.1063-14T>A +NF1 NM_000267:c.1063-1G>T +NF1 NM_000267:c.1063-2A>G +NF1 NM_000267:c.1063-2A>T +NF1 NM_000267:c.1093_1094del +NF1 NM_000267:c.1094C>G +NF1 NM_000267:c.1105C>T +NF1 NM_000267:c.1132_1133dup +NF1 NM_000267:c.1133_1136del +NF1 NM_000267:c.1139_1142delinsAAAA +NF1 NM_000267:c.1153del +NF1 NM_000267:c.1185_1185+2del +NF1 NM_000267:c.1185+1G>A +NF1 NM_000267:c.1185+1G>C +NF1 NM_000267:c.1185+1G>T +NF1 NM_000267:c.1185+2_1185+3delinsG +NF1 NM_000267:c.1185G>A +NF1 NM_000267:c.1186-1del +NF1 NM_000267:c.1186-2A>T +NF1 NM_000267:c.1198C>T +NF1 NM_000267:c.1202del +NF1 NM_000267:c.1212del +NF1 NM_000267:c.1226_1227del +NF1 NM_000267:c.1235A>G +NF1 NM_000267:c.1241T>G +NF1 NM_000267:c.1246C>T +NF1 NM_000267:c.1260+1544A>G +NF1 NM_000267:c.1260+1604A>G +NF1 NM_000267:c.1260+1G>A +NF1 NM_000267:c.1260+2dup +NF1 NM_000267:c.1260+3A>T +NF1 NM_000267:c.1260+4A>T +NF1 NM_000267:c.1260+5G>A +NF1 NM_000267:c.1260+5G>C +NF1 NM_000267:c.1260G>A +NF1 NM_000267:c.1261-1G>A +NF1 NM_000267:c.1261-2A>C +NF1 NM_000267:c.1261-2A>G +NF1 NM_000267:c.1274G>A +NF1 NM_000267:c.1275G>A +NF1 NM_000267:c.1278G>A +NF1 NM_000267:c.127del +NF1 NM_000267:c.1299T>A +NF1 NM_000267:c.1301del +NF1 NM_000267:c.1302T>A +NF1 NM_000267:c.1318C>T +NF1 NM_000267:c.1329del +NF1 NM_000267:c.132del +NF1 NM_000267:c.134A>G +NF1 NM_000267:c.1360del +NF1 NM_000267:c.1378A>G +NF1 NM_000267:c.1381C>T +NF1 NM_000267:c.1392+1G>T +NF1 NM_000267:c.1393-2A>G +NF1 NM_000267:c.1393-591A>G +NF1 NM_000267:c.1393-592A>G +NF1 NM_000267:c.1393-7_1393-1delinsC +NF1 NM_000267:c.1393-9T>A +NF1 NM_000267:c.1399dup +NF1 NM_000267:c.1411A>T +NF1 NM_000267:c.1414del +NF1 NM_000267:c.1460_1461delinsT +NF1 NM_000267:c.1465_1466delinsC +NF1 NM_000267:c.1465dup +NF1 NM_000267:c.1466A>G +NF1 NM_000267:c.1467_1468dup +NF1 NM_000267:c.147C>G +NF1 NM_000267:c.147del +NF1 NM_000267:c.1527+1159C>T +NF1 NM_000267:c.1527+1G>A +NF1 NM_000267:c.1527+1G>C +NF1 NM_000267:c.1527+1G>T +NF1 NM_000267:c.1527+2dup +NF1 NM_000267:c.1527+4_1527+7del +NF1 NM_000267:c.1527+5_1527+6delinsA +NF1 NM_000267:c.1527+5G>A +NF1 NM_000267:c.1528-14_1546del +NF1 NM_000267:c.1541_1542del +NF1 NM_000267:c.1541del +NF1 NM_000267:c.1570G>T +NF1 NM_000267:c.1591_1602delinsA +NF1 NM_000267:c.1592_1595dup +NF1 NM_000267:c.1607C>A +NF1 NM_000267:c.1639G>T +NF1 NM_000267:c.1641+1G>A +NF1 NM_000267:c.1641+2T>A +NF1 NM_000267:c.1642-10A>G +NF1 NM_000267:c.1642-1G>C +NF1 NM_000267:c.1642-2A>G +NF1 NM_000267:c.1642-449A>G +NF1 NM_000267:c.1642-5T>G +NF1 NM_000267:c.1649T>C +NF1 NM_000267:c.1651del +NF1 NM_000267:c.1655T>G +NF1 NM_000267:c.1658A>G +NF1 NM_000267:c.1663_1666del +NF1 NM_000267:c.1665dup +NF1 NM_000267:c.1676T>A +NF1 NM_000267:c.1679del +NF1 NM_000267:c.1708del +NF1 NM_000267:c.1720A>C +NF1 NM_000267:c.1721+1G>A +NF1 NM_000267:c.1721+1G>C +NF1 NM_000267:c.1721+1G>T +NF1 NM_000267:c.1721+2T>C +NF1 NM_000267:c.1721+3A>G +NF1 NM_000267:c.1721+537T>G +NF1 NM_000267:c.1721+542A>G +NF1 NM_000267:c.1721G>A +NF1 NM_000267:c.1722-2A>G +NF1 NM_000267:c.1722-3C>G +NF1 NM_000267:c.1728_1729del +NF1 NM_000267:c.174_177del +NF1 NM_000267:c.1743delinsCA +NF1 NM_000267:c.1748A>G +NF1 NM_000267:c.1755_1756del +NF1 NM_000267:c.1756_1759del +NF1 NM_000267:c.1756del +NF1 NM_000267:c.1758_1759del +NF1 NM_000267:c.1758del +NF1 NM_000267:c.1772_1781del +NF1 NM_000267:c.1783_1784del +NF1 NM_000267:c.1783G>T +NF1 NM_000267:c.179_181del +NF1 NM_000267:c.1797G>A +NF1 NM_000267:c.1809del +NF1 NM_000267:c.1811T>A +NF1 NM_000267:c.1837_1841del +NF1 NM_000267:c.1837_1845+17del +NF1 NM_000267:c.1838_1841del +NF1 NM_000267:c.1842_1845+1del +NF1 NM_000267:c.1845+1G>T +NF1 NM_000267:c.1845+2T>A +NF1 NM_000267:c.1845+2T>C +NF1 NM_000267:c.1845G>T +NF1 NM_000267:c.1846C>T +NF1 NM_000267:c.1849del +NF1 NM_000267:c.1854_1857del +NF1 NM_000267:c.1882dup +NF1 NM_000267:c.1885G>A +NF1 NM_000267:c.1888del +NF1 NM_000267:c.1889G>A +NF1 NM_000267:c.1896T>A +NF1 NM_000267:c.1914_1917dup +NF1 NM_000267:c.1933A>G +NF1 NM_000267:c.1945G>T +NF1 NM_000267:c.1A>G +NF1 NM_000267:c.2002-19_2005del +NF1 NM_000267:c.2013_2014delinsC +NF1 NM_000267:c.2027del +NF1 NM_000267:c.2031_2093del +NF1 NM_000267:c.2033_2034delinsC +NF1 NM_000267:c.2033del +NF1 NM_000267:c.2033dup +NF1 NM_000267:c.2038del +NF1 NM_000267:c.204+1G>A +NF1 NM_000267:c.204+1G>T +NF1 NM_000267:c.2041C>T +NF1 NM_000267:c.2050C>T +NF1 NM_000267:c.205-1G>C +NF1 NM_000267:c.205-2A>G +NF1 NM_000267:c.2072_2076dup +NF1 NM_000267:c.2072T>G +NF1 NM_000267:c.2077_2078del +NF1 NM_000267:c.2084T>G +NF1 NM_000267:c.2087G>A +NF1 NM_000267:c.2131del +NF1 NM_000267:c.2140_2150del +NF1 NM_000267:c.2172dup +NF1 NM_000267:c.2173G>T +NF1 NM_000267:c.2205_2206dup +NF1 NM_000267:c.2246C>G +NF1 NM_000267:c.2251+1G>A +NF1 NM_000267:c.2251+2T>C +NF1 NM_000267:c.2251+2T>G +NF1 NM_000267:c.2251G>A +NF1 NM_000267:c.2252-2A>C +NF1 NM_000267:c.2252-30_2252-6delinsT +NF1 NM_000267:c.2252-3T>G +NF1 NM_000267:c.2256_2259dup +NF1 NM_000267:c.2266C>T +NF1 NM_000267:c.2269A>T +NF1 NM_000267:c.2271_2272del +NF1 NM_000267:c.2272del +NF1 NM_000267:c.2288T>C +NF1 NM_000267:c.2303_2304del +NF1 NM_000267:c.2304_2308del +NF1 NM_000267:c.2310_2314del +NF1 NM_000267:c.232_233del diff --git a/testVar.vcf b/testVar.vcf new file mode 100644 index 0000000..8dce6fb --- /dev/null +++ b/testVar.vcf @@ -0,0 +1,23 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 +20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 +20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 +20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3