Re: [svtoolkit-help] An recalibration problem

[Bob H. <han...@br...>]

This is a question about GATK, not about SVToolkit.
You should post this at GetSatisfaction at http://getsatisfaction.com/gsa
-Bob

On 6/29/11 1:41 AM, sunchangyue wrote:
> Hi,
> Why do I still get this erro even though all reads have RG tag in sam.
>
> ##### ERROR MESSAGE: SAM/BAM file 
> SAMFileReader{/share/data/staff/sunchy/BFC2011010/HL040/GATK/test_HL040_1_pair_NM2_header.sorted.rmdup.bam} 
> is malformed: The input .bam file contains reads with no read group. 
> First observed at read with name = 
> HWI-ST298:171:81MJKABXX:6:1101:11277:2454 Users must set both the 
> default read group using the --default_read_group <String> argument 
> and the default platform using the --default_platform <String> argument.
>
> and here is the  sam:
> @SQ     SN:1    LN:249250621
> @SQ     SN:2    LN:243199373
> @SQ     SN:3    LN:198022430< /span>
> @SQ     SN:4    LN:191154276
> @SQ     SN:5    LN:180915260
> @SQ     SN:6    LN:171115067
> @SQ     SN:7    LN:159138663
> @SQ     SN:8    LN:146364022
> @SQ     SN:9    LN:141213431
> @SQ     SN:10   LN:135534747
> @SQ     SN:11   LN:135006516
> @SQ     SN:12   LN:133851895
> @SQ     SN:13   LN:115169878
> @SQ     SN:14   LN:107349540
> @SQ     SN:15   LN:102531392
> @SQ     SN:16   LN:90354753
> @SQ     SN:17   LN:81195210
> @SQ     SN:18   LN:78077248
> @SQ     SN:19   LN:59128983
> @SQ &nb sp;   SN:20   LN:63025520
> @SQ     SN:21   LN:48129895
> @SQ     SN:22   LN:51304566
> @SQ     SN:X    LN:155270560
> @SQ     SN:Y    LN:59373566
> HWI-ST298:171:81MJKABXX:6:1101:1664:2484        83      10     
>  42832500        37      63M     =       42832371        -192   
>  AATTATATTTAGTAAAGCTTAACAACCAATAAAAGGCTTTACCACATTC
> TTCGAATTTGTAAG 
>  DC<48**?0*@?**?B9*??3@GFCAE9IIIIGEEHGEHCF9B<<GHGHGHHHBHFFFFFCC@ 
> RG:Z:FLOWCELL1-LINE1    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  M
> D:Z:6G56        RG:Z:READ_GROUP_1
> HWI-ST298:171:81MJKABXX:6:1101:1664:2484        163     10     
>  42832371        36      50M     =       42832500        192     
> AGCTTTGCCACATTCTTCACATTTGCAGGGTTTCTCTCCCGTACGAATT
> C       @@BDFB>?B?BHHIFEGCEHF9EE><AFEGCEH9<???F*00))00?FHG     
>  RG:Z:FLOWCELL1-LINE1    XT:A:R  NM:i:1  SM:i:0 &n bsp;AM:i:0  X0:i:5 
>  X1:i:3  XM:i:1  XO:i:0  XG:i:0  MD:Z:43T6       R
> G:Z:READ_GROUP_1
> HWI-ST298:171:81MJKABXX:6:1101:2442:2401        99      13     
>  101256483       60      49M     =       101256650       230     
> GTAACAAAAATAAAGATGTGAGGCTGCCTGCTCTTGCCTAAAGCATGGC
>         @@@FFFFDDDHHHBHBGGC4AFGICB;AFG>3?<D@F;CD@GH**09?@       
> RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1  X1:i:0 
>  XM:i:0  XO:i:0  XG:i:0  MD:Z:49 RG:Z:READ
> _GROUP_1
> HWI-ST298:171:81MJKABXX:6:1101:2442:2401        147     13     
>  101256650       60      63M     =       101256483       -230   
>  GAGAAAAGCATATAGATATTCTATGTTAAAACTTCCATTCCTCATTCGA
> TTATTTGCCCTATT 
>  HC83<GFB899FB499?00*EFGF>GB???1HEEGE9E@EIHHCGGFCCAFADD;;FFFD@@< 
> RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:2  SM:i:37 AM:i:37 X0:i:1  X1:i:0 
>  XM:i:2  XO:i:0  XG:i:0  M
> D:Z:1G17A43     RG:Z:READ_GROUP_1
> HWI-ST298:171:81MJKABXX:6:1101:2496:2427        83      2 0     
>  49195046        60      65M     =       49194943        -168   
>  TCTTTTCAAAGTCCGAGAGTCAGGGTCACTCAGCCCGGAGCACGGGCCC
> GTTGTGGTGCACTGCA       
>  ?:5(55;3ABA:FFCBECHC?>>ACDF@IGHBF6IJJJJIGGGGHBHJIGHGFGHHHDDDFFC@@     
>   RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1 
>  X1:i:0  XM:i:0  X
> O:i:0   XG:i:0  MD:Z:65
> HWI-ST298:171:81MJKABXX:6:1101:2496:2427        163     20     
>  49194943        60      60M     =       49195046        168     
> TTTTTCTCTTTCAGACCCAAGAAACTCGAGAGATCTTACATTTCCACTA
> TACCACATGGC     
> @@@FFE?DDHFFFGDEEBEE;BCE<C9CAC@F19CF**:*?****0*00?9B9B328B>D   
>  RG:Z:FLOWCELL1-LINE1    XT:A:U  NM:i:0  SM:i:37 AM:i:37 X0:i:1 
>  X1:i:0  XM:i:0  XO:i:0  XG:i:0  M
> D:Z:60  RG:Z:READ_GROUP_1
>
> My commander line is :
> /usr/java/jdk1.6.0_16/bin/java -jar 
> /share/apps/GenomeAnalysisTK-1.0.5777/GenomeAnalysisTK.jar -l INFO -R 
> /share/data/staff/sunchy/data/GATK/human_g1k_v37.fasta --DBS NP 
> /share/data/staff/sunchy/data/GATK/dbsnp_129_b37.rod -I 
> sorted.rmdup.bam -T CountCovariates -cov ReadGroupCovariate -cov 
> QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate 
> -recalFile var.csv
>
> Thank you
>                                       Cheo
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help