MAPQ should be 0 for unmapped read.

Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. MAPQ should be 0 for unmapped read.; File chrm.sam; Line 1477
Line: HWI-ST499:5:23:21302:167400#GCCAAT    87    chrM    16518    60    55M    =    16319    -254    GGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGG    bSbcWbccc_^b\_]da_ddcbcQcUfefcffffccdddde_eebffdddfaefd    XT:A:U    NM:i:2    XN:i:1    SM:i:37    AM:i:25    X0:i:1    X1:i:0    XM:i:2    XO:i:0    XG:i:0    MD:Z:3C50C0

 

sourceforge.net/mailarchive/forum.php?thread_name=4B957356.2000202@broadinstitute.org&forum_name=samtools-devel

 

> >>>>>>>> Exception in thread "main"
> >>>>>>>> net.sf.samtools.SAMFormatException: Error
> >>>>>>>> parsing text SAM file. MAPQ must should be 0 for unmapped  
> >>>>>>>> read.;
> >>>>>>>> File sorted.sam; Line 8910023
> >>>>>>>> Line: ./S2:747_1696_219 4 chr18 90771994 25 48M * 0 0
> >>>>>>>> AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGTTTGGGGCTT
> >>>>>>>> ]]]]]]PLQ]]XW[]QA6H]]VI+3]M9FSIFG@... XT:A:U
> >>>>>>>> CM:i:1 XN:i:
> >>>>>>>> 10 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:40C7
> >>>>>>>>
> >>>>>> You don't say what creature this is or how long its chr18
> >>>>>> sequence is, but
> >>>>>> this looks a lot like our favourite bwa "feature" in which
> >>>>>> spurious
> >>>>>> mappings bridging adjacent reference sequences are marked as
> >>>>>> unmapped but
> >>>>>> otherwise left intact (see the FAQ at http://bio

-
> >>>>>> bwa.sourceforge.net/ ).
> >>>>>>
> >>>>>> It would appear that bwa's leaving such non-mappings with a non-
> >>>>>> zero MAPQ
> >>>>>> and non-empty CIGAR conflicts with Picard's validity checking.
> >>>>>> (And other
> >>>>>> non-zero/empty fields are not great either, but those are the
> >>>>>> main ones
> >>>>>> that Picard currently checks.)
> >>>>>>
> >>>>>> Depending on your reference, this may or may not explain your
> >>>>>> particular
> >>>>>> problem.  Is your chr18 reference about 90772000 bases?
> >>>>>>
> >>>>>> (Also: picard typo :-))
> >>>>>>
> >>>>>> Cheers,
> >>>>>>
> >>>>>>  John
> >>>>>>


	
	
	
	
	
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HWI-ST499:5:23:21302:167400#GCCAAT

87

chrM

16518

60

55M

=

16319

-254

GGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGG

bSbcWbccc_^b\_]da_ddcbcQcUfefcffffccdddde_eebffdddfaefd

XT:A:U

NM:i:2

XN:i:1

SM:i:37

AM:i:25

X0:i:1

X1:i:0

XM:i:2

XO:i:0

XG:i:0

MD:Z:3C50C0

HWI-ST499:5:44:16607:70588#GCCAAT

141

chrM

16476

25

100M

=

16476

0

GTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCggggggggggbffffffefbfffefgdggegbggfeefchff^ffWdcddffefegggffgfgggfgggddffefggggggggfggggegdfgadgegadXT:A:U

NM:i:5

XN:i:4

SM:i:25

AM:i:0

X0:i:1

X1:i:0

XM:i:5

XO:i:0

XG:i:0

MD:Z:45C50C0G0G0G0

HWI-ST499:5:64:19795:166573#GCCAAT

151

chrM

16474

60

100M

=

16387

-187

GGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGA

ddda\f_aegUdfdd]eN`eggedgggg_gageffgggdggggggggggdggggggeeeggggdgffdhedffcecggegfggegfggggggggggdggg

XT:A:U

NM:i:3

XN:i:2

SM:i:37

AM:i:37

X0:i:1

X1:i:0

XM:i:3

XO:i:0

XG:i:0

MD:Z:47C50C0G0

picard (http://picard.sourceforge.net/explain-flags.html) 会检查FLAG的含义如果为： read unmapped，就会报错CIGAR should have zero elements for unmapped read。MAPQ should be 0 for unmapped read 这个主要是在染色体的最后一点，BWA认为一个pair比对上了，另一个也在这个位置但是没有满足条件没有比对上 （如真好在最末尾，referance不够长了，就会产生这个错误。会给一个MAPQ值，和一个read unmapped得FLAGS。） lstFlags = [["read paired", 0x1], ["read mapped in proper pair", 0x2], ["read unmapped", 0x4], ["mate unmapped", 0x8], ["read reverse strand", 0x10], ["mate reverse strand", 0x20], ["first in pair", 0x40], ["second in pair", 0x80], ["not primary alignment", 0x100], ["read fails platform/vendor quality checks", 0x200], ["read is PCR or optical duplicate", 0x400]];