bwa sampe max insert size

zlu · 10-27-2009, 07:35 AM

Dear BWA users,

Checking through the sam file produced from the following commands:

bwa sampe -a 2792 ref.fa read1.sai read2.sai read1.fq read2.fq > read.pe.bwa.sam

I have found a high percentage of pairings with insert size much greater that the 2792bp specified with the -a option (examples belwo). Have anyone seen this and do you have an explanation? Thank you

EBRI093151:5:1:41:1387#0 97 Chr5 117315749 37 36M = 117330940 15227 CTTTTTTTGCCTAACAGTTACTGACAGTCNAAACAC BBBBABBABABBBBA@=7BBBB:@ABA78%8A@>@@ XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:29A6
EBRI093151:5:1:41:1387#0 145 Chr5 117330940 0 36M = 117315749 -15227 TAAAGACAGAAAGGTGAGACAAAATCATACAAGAAT BAA@@?CBBBAA@BBBAB?ABCCBBB?BBCACBCCA XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:4 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:36

EBRI093151:5:1:45:1788#0 113 Chr12 30926022 37 36M = 39099548 8173526 AACAACNCTCAATTGTGGATGTGACATGATGGAAGT B??@>:%=?BBB<A@@AB8BBCB@BA@@BBBBBBBB XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A29
EBRI093151:5:1:45:1788#0 177 Chr12 39099548 0 36M = 30926022 -8173526 AGCATTTTTCATGATGTACTCTGCATATAAGTTAAA @=?BBABBBBBBABBB@@ABBBBB?CBBBBB>BBBA XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:204 XM:i:0 XO:i:0 XG:i:0 MD:Z:36

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10-27-2009, 07:35 AM	#1
zlu Member Location: Southeast Asia Join Date: Nov 2008 Posts: 34	bwa sampe max insert size Dear BWA users, Checking through the sam file produced from the following commands: bwa sampe -a 2792 ref.fa read1.sai read2.sai read1.fq read2.fq > read.pe.bwa.sam I have found a high percentage of pairings with insert size much greater that the 2792bp specified with the -a option (examples belwo). Have anyone seen this and do you have an explanation? Thank you EBRI093151:5:1:41:1387#0 97 Chr5 117315749 37 36M = 117330940 15227 CTTTTTTTGCCTAACAGTTACTGACAGTCNAAACAC BBBBABBABABBBBA@=7BBBB:@ABA78%8A@>@@ XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:29A6 EBRI093151:5:1:41:1387#0 145 Chr5 117330940 0 36M = 117315749 -15227 TAAAGACAGAAAGGTGAGACAAAATCATACAAGAAT BAA@@?CBBBAA@BBBAB?ABCCBBB?BBCACBCCA XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:4 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 EBRI093151:5:1:45:1788#0 113 Chr12 30926022 37 36M = 39099548 8173526 AACAACNCTCAATTGTGGATGTGACATGATGGAAGT B??@>:%=?BBB<A@@AB8BBCB@BA@@BBBBBBBB XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A29 EBRI093151:5:1:45:1788#0 177 Chr12 39099548 0 36M = 30926022 -8173526 AGCATTTTTCATGATGTACTCTGCATATAAGTTAAA @=?BBABBBBBBABBB@@ABBBBB?CBBBBB>BBBA XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:204 XM:i:0 XO:i:0 XG:i:0 MD:Z:36