基因数据处理12之samtool的tview来查看sam的匹配文件

基因数据处理12之samtool的tview来查看sam的匹配文件

具体的之前有文章讲过：http://blog.csdn.net/xubo245/article/details/50836185

记录：

1.

运行

?samtools tview SRR003161h20Sorted.bam GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna

输入‘/’后会弹出goto：，然后再输入：chr1:143217889

2.bam中的信息：

hadoop@Master:~/cloud/adam/xubo/data/test20160310$ samtools view SRR003161h20.bam
SRR003161.1	0	chr1	143217889	0	4S35M85S	*	0	0	TCAGATGCAATCATCGAATGGTCTCGAATGGAATCNTCTANAGAGATGGAATGTATCNCTCGCCANACGACACNCGAACAGGGNAAGGCAAGCAGNAGGNAGNNNANNNNNNNNNNNNNNNNNN	AAAAAAAAAAAAAAAA:::BAAFAABAAB?>>=44!39=<!:866699888220862!08:8002!0200000!022200800!20660000600!000!06!!!6!!!!!!!!!!!!!!!!!!	NM:i:1	MD:Z:31A3	AS:i:3XS:i:33	XA:Z:chr10,+42092546,4S35M85S,1;chr1,+143217421,+143239587,-143252938,85S35M4S,+143220601,+143219665,-143210830,1;chr10,+42075371,+42101425,+143272381,-143204112,+143189975,+42080829,+42067652,+143236600,+42071261,+143202568,+143262016,+42094445,+143229991,+143194906,+42098197,+143229325,+143273144,+143236132,1;chr3,-196898795,-125173710,+42074903,+143193143,+143190443,+42085796,+143224622,+143267943,+42103854,+143225093,-143249828,+143231300,-143256486,-143209440,+143228021,+143185063,-41852367,-143251629,+143233540,+42093977,+143200517,+143194441,+42070793,+143206914,+143237811,+143227553,-143255189,+143231768,+143271341,+42080361,+143213870,+42074435,+143263324,+42097745,+42090276,-125180284,+143240055,+143265756,+143216113,-125169985,+143219197,+143192675,+42095848,+143195374,+143214338,+143270772,-125166285,+143275099,+143226451,+42104319,+143232233,+143211626,+143220133,+143215645,+42100036,-41846998,-125168084,-125179816,+143240523,+143264771,+143212094,4S34M86S,-41845898,86S34M4S,+143191375,4S31M89S,0;chr1,-125182919,89S31M4S,+143221908,+143190911,0;chr10,-41843753,0;chr10_KI270824v1_alt,+1080,1;chr10_KI270824v1_alt,+615,1;
SRR003161.2	0	chr7	41381016	60	4S153M1D132M1D5M1D28M1D73M3I12M1I40M54S	*	0	0	TCAGTTTGAGATGGAGTTTCATTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCAATCTCAGCTCACAGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCTCGAGTAGCTGGGATTACAGGCATGCACCATCACGCCCAGCTAATTTGCATTTTTTATTAGAGATGGGGTTTCTCCACATTGGTCAGGCTGATCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCTGAGCCCAACCTATTTACTTTCAATCCATCTTTTCAATAACTTAAATACAAGTGTCAATATATACAATCTTTTCCTCCCTGGTTATCAAGCTTTCTAATATATATGGATGTATCTTCCAAGGTTTTTGATCCCATTTTACTTTACAGGCTCACTGCTGTGGAACCCAGAGAGCAGTCTCTTTTCAAGGNGGGCTGAGACNCGCAACAGGGGATTAGGCCAAGGCNCAGG	CCCCCCCCCCCCCCCC@@@CCCFEEEFEEG888EEEFFEEEEFGGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA<777@@CCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAAACCCCCCCCCCCCCCCCCCCCCCC:93339@A>77//39AC666666C22CAAAA93333///7-0017>9999>>A???ACCCCCCC2239322>9977<?????CCCCCCCCC877777777222221::::5555:555:::::::::;:555:;;::::0040-----***--467::::;;;;;;:::511155555:555:::;::::::7777744-------///245::;;;::::::;;;;;;;;:55554774----------44-----064---------6---522451115247644255-----,4---24464422---------!,4464224!11:::7:::222221--7777---!----	NM:i:1MD:Z:153^T40T91^T5^T28^G73G23C0G26	AS:i:379	XS:i:88