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
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sourceforge.net/mailarchive/forum.php?thread_name=4B957356.2000202@broadinstitute.org&forum_name=samtools-devel
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> >>>>>>>> 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> >>>>>><!-- BODY,DIV,TABLE,THEAD,TBODY,TFOOT,TR,TH,TD,P { font-family:"DejaVu Sans Condensed"; font-size:x-small } -->HWI-ST499:5:23:21302:167400#GCCAAT87chrM165186055M=16319-254GGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGbSbcWbccc_^b\_]da_ddcbcQcUfefcffffccdddde_eebffdddfaefdXT:A:UNM:i:2XN:i:1SM:i:37AM:i:25X0:i:1X1:i:0XM:i:2XO:i:0XG:i:0MD:Z:3C50C0 HWI-ST499:5:44:16607:70588#GCCAAT141chrM1647625100M=164760GTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCggggggggggbffffffefbfffefgdggegbggfeefchff^ffWdcddffefegggffgfgggfgggddffefggggggggfggggegdfgadgegadXT:A:UNM:i:5XN:i:4SM:i:25AM:i:0X0:i:1X1:i:0XM:i:5XO:i:0XG:i:0MD:Z:45C50C0G0G0G0HWI-ST499:5:64:19795:166573#GCCAAT151chrM1647460100M=16387-187GGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGAddda\f_aegUdfdd]eN`eggedgggg_gageffgggdggggggggggdggggggeeeggggdgffdhedffcecggegfggegfggggggggggdgggXT:A:UNM:i:3XN:i:2SM:i:37AM:i:37X0:i:1X1:i:0XM:i:3XO:i:0XG:i:0MD:Z:47C50C0G0picard (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]];