SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA - XM tag Question Arupsss Bioinformatics 8 06-28-2012 08:22 AM
what wrong with boost? feng Bioinformatics 3 10-16-2011 09:50 AM
how do I output the CS tag for BWA align of SOLID reads? KevinLam Bioinformatics 16 07-23-2011 10:06 PM
mutiple mapped reads FLAG/TAG in bwa alignment data totalnew Bioinformatics 0 05-06-2011 10:21 AM
BWA concise format output -edit distance wrong biterbilen Bioinformatics 2 11-06-2009 02:55 PM

Reply
 
Thread Tools
Old 04-01-2013, 08:49 AM   #1
Lcontami
Junior Member
 
Location: France

Join Date: Feb 2013
Posts: 5
Default BWA : XM tag is sometimes wrong

Hi,
I've been using the XM tag to find reads with no mismatches but sometimes this tag doesn't give the right number of mismatches.
Has someone else had this problem ? How did you fix it ?

Here is a few examples :

HWI-ST0787:100:C02F9ACXX:7:2307:2404:186548 163 gi|83578099:1-1090946 95044 60 37M1D2M1D62M = 95049 108 GGGGTTTCGGAAAACAAACTCGCTCGATACAGTAATTGCGTTTTATTTACGGAAATTACCGTTCTCGGTTCCAAGAAGGTTAGAAAAATCGGTTGTCGCTC +1+4+0=D+<CFADB9E@@99:CG:BF)*9?DDDC@D?'-<;@=FHCHDB1?EEBCFEFDDCC;?B=8<35@C9?AA?A:?(:4<8ACBB<995>>158 XT:A:U NM:i:4 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:2 MD:Z:0C1T34^G2^A62

HWI-ST0787:100:C02F9ACXX:7:2307:9817:186685 147 gi|83578099:1-1090946 95060 60 21M1D2M1D78M = 94975 -188 AACTCGCTCGATACAGTAATTGCGTTTTATTTACGGAAATTACCGTTCTCGGTTCCAAGAAGGTTAGAAAAATCGGTTGTCGCTCTTTCTTTCCCCCACTT @9B@DDBBDDEEDDDDDDDDBB<@DCDDDAB<@?:3EDC?<8DDDDBDCA??EBHHHHHHIIIIJIIGGJIHIGIIGJJJIIJIGEIHF;@?1FDDBB?B? XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:21^G2^A78

HWI-ST0787:100:C02F9ACXX:7:2307:17522:186893 83 gi|83578099:1-1090946 999268 60 68M1I31M2D1M = 999191 -179 CCCTGTATAATGAAATTTCAAAAATATTTTCGTGAATAGTGATTTATTTAATTTAAGCACTAAATTATCCTTACGGACTTGGGCTACATTCATGTTTGCAC BCCCCDDCADCCCCCCCCEED?3HEEA;4EAHHEG>FDCB=CIHGIIGGIHFF<DBGIHEGEIGGFF<EGGBCFAFAB?B3HB<BFE9B>DDHD??DA@?1 XT:A:U NM:i:4 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:1 MD:Z:3C95^AG1

HWI-ST0787:100:C02F9ACXX:7:2307:12781:188676 83 gi|50593115:1-813178 389360 60 61M1D3M1D37M = 389271 -192 TTTAACTTATGAATGTACTTTACTGGCCAAGAATCCGTCTGGAACCATTCTACGGTGCTCTTGCTAGCGCTAAAGACAGCTATAGTGGATATTCAGACGGT >DDCCCCC@DDFDCCCBCCCCDBCCAECECDB8HHHIHDA@==)GCGDCFC8GEJIFJFIGHDJGIIGGHIIGGEBJJFHIJIGGHFGGGHHDFDDBF@C@ XT:A:U NM:i:3 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:2 MD:Z:61^C1T1^G37
Lcontami is offline   Reply With Quote
Old 04-01-2013, 09:21 AM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default BWA : XM tag is sometimes wrong

from the CIGAR strings for the reads in your examples, it looks like you have some deletions or insertions, but not mismatches.
mastal is offline   Reply With Quote
Old 04-01-2013, 09:25 AM   #3
Lcontami
Junior Member
 
Location: France

Join Date: Feb 2013
Posts: 5
Default More details

HWI-ST0787:100:C02F9ACXX:7:2307:2404:186548 163 gi|83578099:1-1090946 95044 60 37M1D2M1D62M = 95049 108 GGGGTTTCGGAAAACAAACTCGCTCGATACAGTAATTGCGTTTTATTTACGGAAATTACCGTTCTCGGTTCCAAGAAGGTTAGAAAAATCGGTTGTCGCTC +1+4+0=D+<CFADB9E@@99:CG:BF)*9?DDDC@D?'-<;@=FHCHDB1?EEBCFEFDDCC;?B=8<35@C9?AA?A:?(:4<8ACBB<995>>158 XT:A:U NM:i:4 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:2 MD:Z:0C1T34^G2^A62

For example in this line, we have 2 deletions and 2 mismatches (see the MD tag). It sums to an edit distance of 4 (in accordance to the NM tag)
However, the XM tag is equal to 3, whereas it should be 2.
Lcontami is offline   Reply With Quote
Old 04-01-2013, 11:04 AM   #4
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default BWA : XM tag is sometimes wrong

Quote:
Originally Posted by mastal View Post
from the CIGAR strings for the reads in your examples, it looks like you have some deletions or insertions, but not mismatches.
sorry, my error, M in the CIGAR string means match or mismatch.
mastal is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO