Experiments on sanity check

Author: Fang Zhang
Date: 2016.6.18
E-mail: fza34@sfu.ca

Experiment 20160618

Merge all unresistant vcf files. 9772 SNPs in total.

vcf-merge $(ls -1 *unresi.vcf.gz | perl -pe 's/\n/ /g') >merge.vcf

Veryfy whether intersection between merge.vcf and Resi-List-MasterV27_.vcf is empty. (Indeed empty)

cat merge.vcf | grep Mycobacterium |awk '{print $2}' > merge.txt
cat ../../../input/RESI_SNPs/Resi-List-MasterV27_.vcf | grep Mycobacterium | awk '{print $2}' > resi.txt
cat merge.txt resi.txt|sort -u|uniq -d

For sample in different experiments, intersection should be in 95%. Results are as below:


samples	GATK	MPILEUP	INTERSECTION	SNP	experiment number	inter	propotion
ERR551821	1476	2098	1429	24	2	1344	0.8813
ERR551822	1502	2189	1440	23	2	1344	0.8813
ERR552910	1443	1531	1406	22	2	1339	0.9234
ERR552911	1424	1545	1383	21	2	1339	0.9234
ERR550782	1475	2140	1427	23	2	1338	0.8826
ERR550783	1480	2117	1427	23	2	1338	0.8826
ERR552493	1501	2251	1441	21	2	1326	0.8549
ERR552494	1479	2021	1436	21	2	1326	0.8549
ERR550658	1451	2033	1401	23	2	1325	0.8576
ERR550659	1516	2301	1469	23	2	1325	0.8576
ERR551956	1443	1602	1391	24	2	1325	0.9305
ERR551957	1418	1567	1358	24	2	1325	0.9305
ERR551167	1400	1459	1365	24	2	1318	0.9166
ERR551168	1429	1528	1391	23	2	1318	0.9166
ERR552939	1497	2482	1457	23	2	1318	0.7993
ERR552940	1556	2261	1510	23	2	1318	0.7993
ERR550940	1488	1629	1404	21	2	1316	0.9139
ERR550941	1406	1547	1352	21	2	1316	0.9139
ERR553081	1395	1544	1357	19	2	1307	0.9108
ERR553082	1444	1679	1385	17	2	1307	0.9108
ERR551680	1448	1593	1389	20	2	1304	0.9049
ERR551681	1421	1530	1356	19	2	1304	0.9049
ERR551155	1453	1665	1378	23	2	1299	0.9116
ERR551156	1387	1467	1346	22	2	1299	0.9116
ERR551369	1451	1600	1368	18	2	1297	0.9102
ERR551370	1426	1589	1355	19	2	1297	0.9102
ERR551693	1421	1573	1366	22	2	1294	0.9106
ERR551694	1409	1517	1349	22	2	1294	0.9106
ERR552549	1436	1603	1355	20	2	1288	0.9167
ERR552550	1387	1437	1338	20	2	1288	0.9167
ERR551854	1353	1511	1317	19	2	1287	0.9226
ERR551855	1423	1571	1365	19	2	1287	0.9226
ERR551927	1389	1492	1337	20	2	1285	0.9094
ERR551928	1423	1540	1361	20	2	1285	0.9094
ERR551977	1377	1523	1332	18	2	1284	0.9126
ERR551978	1414	1548	1359	19	2	1284	0.9126
ERR550946	1402	1566	1344	20	2	1283	0.923
ERR550947	1379	1576	1329	20	2	1283	0.923
ERR553156	1411	1552	1375	18	2	1272	0.9034
ERR553157	1355	1507	1325	19	2	1272	0.9034
ERR552894	1431	1559	1365	20	2	1266	0.9004
ERR552895	1337	1440	1307	19	2	1266	0.9004
ERR551804	1443	1722	1401	24	3	1258	0.8359
ERR551805	1373	1476	1352	24	3	1258	0.8359
ERR551806	1395	1557	1357	24	3	1258	0.8359
ERR551360	1464	1741	1422	23	3	1249	0.8201
ERR551361	1420	1570	1378	23	3	1249	0.8201
ERR551362	1401	1632	1363	24	3	1249	0.8201
ERR553303	1320	1386	1298	26	2	1247	0.8926
ERR553304	1388	1467	1346	26	2	1247	0.8926
ERR553274	1398	1652	1330	18	2	1246	0.9075
ERR553275	1334	1479	1289	18	2	1246	0.9075
ERR552444	1394	1622	1362	18	2	1243	0.8735
ERR552445	1343	1579	1304	18	2	1243	0.8735
ERR551556	1435	1755	1400	24	3	1220	0.8193
ERR551557	1335	1433	1317	23	3	1220	0.8193
ERR551558	1354	1589	1329	21	3	1220	0.8193
ERR550643	1291	1397	1266	18	2	1217	0.9157
ERR550644	1328	1490	1280	17	2	1217	0.9157
ERR550777	1375	1585	1342	23	3	1217	0.8262
ERR550778	1420	1565	1372	25	3	1217	0.8262
ERR550779	1335	1526	1324	24	3	1217	0.8262
ERR551184	1380	1558	1337	17	2	1205	0.8644
ERR551185	1291	1465	1262	18	2	1205	0.8644
ERR551943	1256	1339	1239	21	3	1194	0.8122
ERR551944	1446	1580	1377	23	3	1194	0.8122
ERR551945	1449	1537	1405	24	3	1194	0.8122
ERR552689	1423	1533	1375	20	2	1131	0.7965
ERR552690	1211	1268	1176	18	2	1131	0.7965
ERR552668	1304	1419	1291	23	4	1056	0.649
ERR552669	1269	1504	1248	21	4	1056	0.649
ERR552670	1419	2009	1392	22	4	1056	0.649
ERR552671	1440	2160	1393	21	4	1056	0.649
ERR551979	1139	1196	1118	15	5	764	0.5128
ERR551980	1295	1456	1272	18	5	764	0.5128
ERR551981	1247	1304	1204	17	5	764	0.5128
ERR551982	1353	1483	1312	18	5	764	0.5128
ERR551983	1061	1116	1041	15	5	764	0.5128